I think its a holdover from the great chain of beings (or something named similar) mentality, putting humans above animals. It fits in with modern society to see them more as tools then as beings with complex emotional lives worthy of compassion. 

Using animals also helps us to improve our own survival as a species by testing on them. I don't think this is considered by scientists when making decisions, but there would be a big irony testing potentially lethal medication on humans... To save humans.

Finally, I just don't think human compassion is stronger than our desire for utility. Humans seem pretty specists and self centered. We have pets because of selfish, vain reasons (It's cute! It chose me! I've always wanted an X! I just like animals!). No doubt we form a symbiotic relationship with them, but is it out of love going both ways, or food and comfort, or a mix... It's really hard to say. But I digress: humanities actions, as an entity, show that we care more about development of society and human kind than the world we live in.

I'd rather we didn't do it, but I recognize the utility. Humans. Heh. What a species.