Pet fees are among the junkiest of junk fees. Consider that I can bring an infant on my lap for free, but it's $100-ish to bring the dog under the seat.
I can see charging something, though, not to compensate the airline for extra service (since there really is none), but to deter the behavior. I think neither the airline nor the flying public wants to have a cabin full of underseat pets, and having a relatively nominal fee helps limit the number of pax who bring the pets along.