DICLAIMER: There is no insinuation attached to this honest question.
Do most animal rights activists pick and choose which animals count as animals, or are they relatively Jainist when it comes to that kind of thing? I mean, do you still kill flies, mosquitoes, etc.?
An excellent question, Johnny. Just as in mainstream culture, there is no consensus among activists. According to ethicists like Singer, who most activists are familiar with, the most important criterion when establishing our treatment of other individuals (ranging from those nearly identical to us to members of different genders, races, creeds, ideologies, intelligences, and yes, species) is to cause as little harm as possible to anyone who has interests (i.e., water, or maximization of happiness) that deserve to be protected. Just as most Americans accept that individual humans with down syndrome deserve equal consideration of interest and, (almost) just the same, that dogs and cats have the capacity for a wide range of thought and emotions, we each therefore have interests which are rightly
Singer also adopts the concept of erring on the side of caution. For example, if there isn't scientific consensus on whether or not a member of a given species (or ... whatever criterion) is sentient, but it is reasonable to think that they may be, treat them as if they are. Except in very special circumstances (say, week 13 of pregnancy), Singer finds that this "just-in-case consideration" is a maximization of justice.
So to your question. Most activists that I know really care about their interaction with others and consider these issues at great depth. Since most activists probably also possess ethics of striving for environmental sustainability and related principles, they seek to cause only positive effects on the lives of all animals (including humans and bees), and attempt to minimize destruction towards other life (including insects, trees and members of the executive branch).
PETA is evil and has a history of its members harming animals (like "liberating" them from labs and then leaving them in dumpsters), and does a huge disservice to animal rights by delegitimizing the entire cause with their insanity.
It is deeply unfortunate that a legitimate and just movement is discredited, for sure. But does the discrediting stem from actions of members of PETA?
Evil? Animals liberated from labs just to be condemned to a dumpster? A "history" of this sort of behavior?
There are public relations organizations like the center for consumer freedom (and their activistcash.com), nothing more than a front-group for tobacco, alcohol and other massive business interests -- seriously, they're opposed to Mothers Against Drunk Driving and the Union of Concerned Scientists. Maybe you got your info from somewhere like here, or from their ripple effects? Just as with the movement toward racial equality, a very vocal minority currently resist considering ideas of ethical treatment of animals with great vigor; perhaps you heard an untruth from someone in this camp, someone more interested in condemning their perceived opponent than considering the issues at hand?
There is a complicated case of two PETA employees that disposed of the bodies of (humanely euthanized) dogs and cats who in a dumpster -- a wrong which attracted tons of attention. While their actions were wrong, however, there is a case that the mission they were serving is ethically justifiable. This one circumstance, moreover, does not constitute a history, or evilness, in my opinion.
EE, you're right, most people probably think of PETA. I wish I knew why! There are a ton of people and philosophies -- even among activists -- not represented by the organization. In fact, the movement for animal protection is as heterogeneous than many other social justice causes, if not more so.