Well, I think it was a few things, yes I think at the time, with the exception of the EXTREME fans who will never get tired of Trek, were tired of Trek by the time Enterprise started, that was part of it.
Because I can say many people enjoy Enterprise today much more than they did when it was being made.
The next issue I think was that, Enterprise basically did re-write the Star Trek history books, and that isn't a complaint from me personally, I really love what Enterprise did personally. I feel that Enterprise is a much better beginning to the story than TOS is. TOS doesn't even feel like the beginning to me. And that isn't a stab at TOS either, I love TOS as well, and view it as another chapter of the Trek story.
But many people didn't take kindly to the idea that Captain Kirk wasn't really the first captain, and the NCC-1701 wasn't the first Enterprise. But I have an argument for that, which I will get to in a minute.
Enterprise also felt very different from the other series, and I think this had to do with two things, there was no Federation, and their ship and technology was extremely limited in comparison to the other series.
I think some people got frustrated seeing the NX-01 crew stumped by problems that any of the other crews could have easily solved.
And not having the Federation and not having the Prime Directive and really not having quite as many species in Enterprise just made it feel very different. But it was by no means bad.
Enterprise isn't my favorite series, but I still enjoy it very much.
I like that Enterprise takes certain issues that the other series couldn't touch on because of the Prime Directive and showed us exactly why the Prime Directive was neccessary.
There were certain stories that only Enterprise could do. Same as there were certain stories that only DS9 could do, and Voyager and so forth.
Every series had something unique about it, and Enterprise was no different.
But here's my thing about the continuity issue. I think the other series can still say Kirk's ship was the first Enterprise, and not talk about Archer's ship, because Archer's ship first of all was only a proto type. All NX Class ships were proto types. In DS9 the Defiant even has an NX registry as it too was a prototype.
If you read the new Federation First 150 Years book that came out recently, that gives alot of very good detailed information that you don't get in the series. Sure you can say it isn't canon, but it was written by a writer from Enterprise, and it goes hand in hand with Trek canon. It doesn't violate anything, it simply adds to it.
Archer's ship predates the Federation.
So yes you can say that Kirk's ship was the first Enterprise under the United Federation of Planets. Which is when ships started getting the NCC registry.
Many people also say, why did we never hear of the Xindi again? Why did we never hear of the Suliban or the Denobulans again? Well I ask, why didn't we hear about the several other species that we only saw once? Or other species that we only saw in one series? Some species were kept and some were dropped.
And why do we never hear of the Xindi?
Do you ask today in 2013 why we never hear of some historical event from 1813? I have no idea what major things were happening in 1813, and for the history buffs who do, is that a major discussion topic?
Bottom line is, it was 200 years ago, and has absolutely nothing to do with our modern day concerns. Same for the TNG onward era.
So all in all, I feel that the majority of fans not liking Enterprise were really just being nit picky, and being resistant to change. TNG, DS9 and Voyager, were all different, but they were also all very similar, and I think people were also used to that. I've heard many people say that Enterprise didn't feel like Star Trek to them. I think it did, it just felt like it was from a different time period.
But I think the number 1 thing people couldn't get passed was that Enterprise became the first series, and TOS isn't anymore. That's something the hardcore TOS fans can never forgive. But as I pointed out, Enterprise shouldn't have been seen as blasphemy to Trek, it should've been seen as a tool to go deeper into Trek's past, and to give us a more detailed beginning as we now have.
People can complain about ENT all they want, but without Enterprise and First Contact we wouldn't know hardly anything prior to TOS. And now with the Federation book I mentioned, we know even more now. We know how we're going to gradually move out of the world we're in and into the world of Trek. Enterprise is essentially the first step in that journey of moving away from modern day into Trek.