>I've been told he has a bad reputation among linguists as being intolerant, brow-beating, and intellectually hyperconservative.
Myself, I'm another "ex-linguist", who studied generative syntax in undergrad with Chomskyans (nowhere near Chomsky himself) in the late 1990s.
Other than the fieldwork issue and the evolution of language/animal communication issue which you've discussed, the subfields of sociolinguistics, computational linguistics, and corpus linguistics also have major disagreements with Chomsky, and have, at various times, received arguably dismissive comments from him. These mostly boil down to the value of "performance data" -- actual samples of language in the world, as opposed to data from introspection-- in developing a model of linguistic competence (the goal of generative linguistics). There were also the "generative semantics wars" of the 1970s, which Frederick Newmayer wrote about in his 1996 book Generative Linguistics: A Historical Perspective (from a Chomskyan perspective).
Because linguistics is a living field, of course, generative linguists often meld Chomsky's theories with those from other subfields, despite Chomsky having said something nasty about that subfield 20-30 years ago. Steven Pinker's (1994) book The Language Instinct gives a good introduction to generative linguistics and linguistics in general, in a way that's a little more open to other subfields in linguistics than Chomsky usually is (FWIW, Pinker appears to be basically a neoconservative politically).
Like Michael said, since Chomsky did revolutionize the discipline in the 1950s, and kept on doing so for 40 years (assuming that minimalist syntax will be the last revolution made by Chomsky himself), scholars do want to make a name for themselves by pointing out his errors, as is only natural in academia. But I think there is a widely-held perception among non-generative-linguists that Chomsky's style of debate and linguistic "intellectual hyperconservatism" has held the field back.
On the other hand, Michael Albert's 2007 memoir "Remembering Tomorrow" might shed some light on Chomsky's "interaction style" and the roots of the perception mentioned above, both in politics and in linguistics. Albert has very graciously serialized several parts of his memoir for free on the http://www.zcommunications.org site. Having known Chomsky personally and politically for decades, Michael Albert writes the following about Chomsky's political interaction style (all quotes from Ch 5, and available here http://www.zcommunications.org/znet/viewArticle/17753 ):
"Noam says what is on his mind, sometimes at a cost. Indeed, bad comes with good. Noam's death grip on the truth can interfere, at times, with other virtues, such as sensitivity to the impact words may have on others. Assessing someone in Noam's position, my tendency is to think truth-telling should take precedence over sensitivity, though others might disagree, and it certainly isn't one size fits all. " ...
"When someone starts to ask Noam something familiar, Noam tends to fill in the blanks, deducing the person's real intent, and interrupting to begin answering sometimes well before the person finishes their question. This can sidetrack Noam's hearing what is actually being said in the interests of saving time and even imposing accuracy. Experience counts and often Noam helps the questioner by making the question more precise and complete. Other times, however, Noam jumps too quickly and misrepresents the questioner, due to thinking he recognizes the questioner when in fact he doesn't. In other words, sometimes a person accosting Noam or disagreeing with him knows more than those who typically use essentially the same initial words. Noam may miss this difference, thereby seeming to be oblivious to the person's true intents and insights. It is not pleasant when it happens to you, and I have undergone it plenty of times, but it is not ill motivated, either." ... "Noam believes strongly in civility, though I think many people who have gotten into debates with him and had their views dismissed or even annihilated—sometimes with words like "stupid" and "trivial" punctuating the dissection—would find that hard to believe. But for Noam, calling an idea stupid or calling a claim trivial is not uncivil but truthful. In this, he is a scientist in the sense that scientists routinely debate and skewer one another in no uncertain terms. Finding the truth and escaping falsehoods, which is the scientist's reason for being, demands this behavior. "
I suppose you could see this as special pleading, or irrelevant to the linguistics question, but I think Chomsky's interaction style might have had an impact on the perception of Chomsky by non-generative linguists.
-Aaron (sorry for the extra-long post, back to lurking)