To the best of my knowledge, the Tau have always had difficulty finding acceptance in some circles of the 40k community.
There are several aspects to the cause of this. The Tau come from a period in 40k's meta-history that is defined by both great change and great controversy. 3rd edition was already a drastic break from the status quo of 2nd edition in terms of rules, atmosphere and - to a lesser extent - aesthetics. The Tau can perhaps be seen as the climax to this series of great changes, being the direct product of a decision by GW to introduce an entirely new faction into 40k and deliberately designed from the outset to be dramatically different to what had come before.
This is important to note, because in my experience a lot of the negativity towards Tau comes from people (commonly, but not always, veterans of 2nd edition or those heavily influenced by veterans of 2nd edition) with a very particular preconception of what 40k should be like. This preconception appears to be based heavily on 2nd edition 40k and how 2nd edition was presented - heavy emphasis on close combat in a science fiction setting, a strong 1980s homage feel, considerable influence from heavy metal music in both atmosphere and style, and a conflict with the Imperium (primarily Space Marines and Imperial Guard) and Chaos with Eldar, Orks and Tyranids as the primary factions. These five were after all the ones there from the start of 2nd edition, and receive the most publicity (not that almost all 40k computer games ever made so far have featured some combination of those five factions right from the start).
The Tau, with their bright idealistic themes, clean high-tech style with strong influences from 1950s, 1960s and 1970s Space Opera and total aversion to melee combat, don't fit into this preconception at all. This is sort of the point - the Tau were after all created to be a contrast to the existing 2nd edition legacy factions. Thus, when the Tau are presented, those holding the above preconception of 40k perceive them as a threat to the setting's identity, which in turn appears to put that vision of 40k that they hold under attack, and respond accordingly.
An analogy of sorts can be seen with the history of my favourite music band, the Finnish symphonic metal group Nightwish. The first lead singer of Nightwish, Tarja Turunen, had a very distinct and unique vocal style, which combined with the equally unique and strong musical style of Nightwish's early albums to form a very unique and distinctive sound which in turn left many fans with a very specific preconception about what Nightwish 'should' sound like. When Nightiwish began to introduce changes to this sound, first musically in the atmosphere of the albums Century Child and Once and then by replacing Tarja Turunen with Anette Olzon between 2006 and 2007, many Nightwish fans felt that their preferred vision of Nightwish had been challenged, and responded with negativity that remains infamous to this day.
It's more or less the same phenomenon at work, and one could almost argue that the Tau are the Anette Olzon of Warhammer 40,000 factions - something very noticeably different to the established status quo that people have come to expect, and is thus perceived as a threat to an ideal that they enjoy. It is from here that you get sentiments along the lines of 'The Tau don't fit with the setting' or 'The Tau aren't Grimdark enough' or 'The Tau should have been killed off long ago' - there's a preconception that 40k's setting should be relentlessly dark with no genuinely good factions or characters, which it seems many enjoy as a setting to explore, and the Tau are seen as a threat to that. While I cannot agree, I do feel as though I might be able to understand the reasoning - I myself have similar reservations about the new range of Space Marines that GW is putting out, as their abundance of safe to operate plasma weaponry and skimmer vehicles appears to me as a threat to my own ideal vision of the Imperium as a backwards crumbling derelict power that doesn't quite realise its dead yet.
Related is the in-game mechanics side of the equation. Much like their drastically different look and feel in the background setting, the Tau have a drastically different playstyle to other 40k factions, with almost no close combat capability at all and an emphasis on mobility and precision shooting attacks. As well as the above phenomena, which can also be applied here, this can make for playing styles and tactics that some find infuriating to play against (Wood Elves in 6th and 7th edition Warhammer Fantasy were in a similar position), which already puts the Tau in a negative light for some circles.
This is further compounded by periods in 40k's history where the Tau have enjoyed a considerable advantage in rules. The Riptides and Supporting Fire of 6th and 7th edition are commonly cited examples of this, but it was also the case in some parts of 4th edition due to rules regarding skimmers and assault - the hatred some have for the 'Fish of Fury' tactic originates from this. Combine this with the grievances outlined above, and you have a centrepiece for ire.
An interesting contrast is the Necrons. The popular C'tan serving life-eradicating 'Oldcron' incarnation of the Necrons is actually newer than the Tau, with their 3rd edition codex and model range being released roughly half a year after the Tau (I for one find the irony hilarious), but because of their more balanced playstyle with a greater emphasis on melee combat and much darker background and atmosphere (indeed, the 3rd edition 'Oldcrons' were created as something of a grimdark antidote to the Tau if the designers' commentary from the time is anything to go by) they are perceived as much less of a threat to what 40k 'should' be like, and thus have gained much wider acceptance by the 40k community. That they had a limited early incarnation in 2nd edition likely helps as well.
A final factor to consider is the power of technology and influence. The years since the original release of the Tau have seen an explosion of new media and communications technology, which in turn has had a dramatic effect on all niche hobby communities. The internet has provided an easy way for hobbyists to communicate with one another regardless of distance or geographic factors, opening up an unheard of level of interaction between circles that beforehand might have been isolated to their own country at most. Likewise, the rise in popularity of computer gaming has given GW a channel to convey their IP to mass audiences that previously only screen media (TV and movies) could have done, while retaining a massive degree of creative control over said IP (something much more difficult to do for TV and movies, where one must navigate production studios, writing teams and executives).
The effects have been powerful. Many people coming into 40k now often have preconceptions of it based on computer games like Dawn of War or Space Marine, which often support the preconceived vision of 40k outlined earlier (notice how almost every 40k computer game project thus far have considered the Imperium, Chaos, Eldar, Orks and Tyranids to be the main focus of 40k factions, with others such as Tau being given a much lower priority for representation). This 'Dawn of War' preconception can then be quickly introduced to the '2nd edition' preconception through the internet as prospective newcommers investigate and research 40k further, and the parallels between the two can allow them to feed into each other.
This then falls into the rise of '1D4chan Canon' (a current working name that I'm giving it until I think of something better). So-called because it is often reflected in that site, if not originating from there, this is a very peculiar perception of 40k that has evolved over the last half-decade or so from what I can only presume to be a combination of memes, the collision of modern video gamer culture with tabletop circles, and widely-propagated opinions among the 40k community that have organically come together in a process not entirely unlike how a Space Hulk is formed. '1D4chan Canon' or '1D4chanism' is difficult to describe to those who have no experience of it, but it is easy to find on the internet - the webseries If The Emperor Had A Text-to-Speech Device and the youtube animated shorts from FlashGitz are both good examples of it in action, and you occasionally see glimpses of it creeping into places as far as Warseer and TVtropes. '1D4chanism' generally seems to have its own idea about the popularity of 40k factions and which ones are more and less acceptable. For whatever reason these ideas have spread and gained popularity. I am unsure whether these views are indeed the most common consensus or are merely actively propagated by an extremely vocal minority.
That's the best guesses that I've been able to make at any rate as to why the Tau seem unpopular.