Scientists are often accused of cruelty towards animals, and there are some experiments that do cause pain…but at the same time, what we can do is very tightly regulated and scrutinized, with every experiment requiring rather thorough justification, and in every case that I know of, the investigators themselves are greatly concerned about minimizing suffering, even without the watchdogs of animal care and use committees hovering over them. And need I mention that scientists actually accomplish something useful in their animal work?
If animal rightists want to focus right now on a widespread practice that causes intense pain, they ought to look to the rules for halal/kosher meat. As Johann Hari explains, there are religious rules that demand that animals needlessly suffer when they are slaughtered, and when criticized, of course the barbarous butchers hide behind the claim that their religion demands this agony.
Atheists who criticise religion are constantly being told we have missed the point and religion is really about compassion and kindness. It is only a handful of extremists and fundamentalists who "misunderstand" faith and use it for cruel ends, we are told with a wagging finger. But here's an example where most members of a religion choose to do something pointlessly cruel, and even the moderates demand "respect" for their "views". Their faith makes them prioritise pleasing an invisible supernatural being over the screaming of actual living creatures. Doesn't this suggest that faith itself - the choice to believe something in the total absence of evidence - is a danger that can lead you up needlessly nasty paths?
It says something about faith that it can be used to justify torture, simply because they've always done it that way.
Oh, and for a beautiful example of misplaced priorities, contrast the insensitivity of the public to slitting the throats of conscious farm animals to this bizarre story of pulling plastic pigs from children's toy sets, because of the possibility that kosher/halal gobbling religionists might be perturbed by the existence of itty-bitty models of smiling swine.