ArsTechnica has an excellent article examining the reasoning behind the violence used by the animal extremist movement.
The issue at its simplest is that animal rights extremists believe that animals are as deserving of the same rights and protections as humans, and that the use of animals in scientific research is deeply immoral. Since animals can’t speak for themselves, the extremist groups use violence on their behalf. Animal rights activists often claim that the use of any animals in research is unnecessary, implying that the researchers who perform such studies are therefore doing it because they must enjoy causing distress.
Other parts of the article are worth quoting at length:
Unfortunately, that argument breaks down under even the simplest scrutiny. As imperfect as animal models are when applied to human biology and disease, putative replacements such as computer simulations remain decades away. We can’t even accurately model the behavior of a single cell on the molecular level due to the thousands of different (but interrelated) biochemical pathways contained within. If a single cell is out of the question, you can imagine that being able to model organs or complete organisms is several magnitudes harder.
Perhaps the problem is our complex relationship with animals. We use them for food, for clothing, as beasts of burden, but also as companions. The habit of anthropomorphizing projects human emotions onto creatures that in many cases are incapable of them; when your dog cranes its head to one side, is it really considering your question thoughtfully, or is it just being a dog?
It’s hard to fathom how passionately misguided you must feel about an issue to resort to inflicting such extreme violence, and in such respects I find little difference between the mentality and goals of religious extremists and animal-rights extremists.