Well, first of all, a headline like "Christian groups oppose stem cell research" will be read and interpreted differently. Since Westerners are very familiar with the diversity of Christian groups, we automatically discount that such a headline is representative of all Christians. The same can't be said for Islam; as many of the comments here show, people are interpreting the headline as if it were representative of Muslims in general.
80,000 on an internet petition IS an insignificant number, especially given (a) that many if not most of the signatories are anonymous and (b) as someone pointed out, many of those who signed the petition left comments stating that they are AGAINST it.
Theo van Gogh's murder was committed by a crazy man who happened to be of Muslim heritage. Many have noted that the murderer didn't fit into Dutch society OR his ancestral Moroccan society-- he was a misfit. So you cannot generalize from his case. No one generalized anything about Christianity when Tim McVeigh killed innocent people in the name of his ideals, nor did anyone criticize the animal rights movement when one of its activists killed Pym Fortuyn. (The Animal rights movement, incidentally, has a record of murderous vandalism.)
As for the Danish cartoon protests -- as Juan Cole (Salon)
has pointed out, the protests were not all that large in size -- perhaps on the scale of football hooliganism in terms of numbers and casualties -- and they weren't primarily motivated by religion, but by various political grievances.
Even the Salman Rushdie case was an exception to the rule. As this Cambridge professor points out, the Sunni world's authorities rejected Khomeini's fatwas
. And most Muslims saw it as a political, not a religious, move on Khomeini's part, to boost his flagging popularity.
Bottom line: Yes, there are some Muslim kooks out there, just as there are kooks in the Western world. And these kooks receive a highly disproportionate share of the media coverage, because (a) Westerners don't know the Muslim world very well, and people fear the unknown, (b) there is a real witch hunt going on in the name of greedy political interests which have a desire to make the Muslim world look bad for their own exploitative purposes. And because of this, we tend to play up the weirdness in the Muslim world, while playing down the awesome amount of violence in our own societies, and the much greater violence we inflict on other societies and have been doing so for the last few hundred years.