I happen to agree with basic pet license fees (obv not for chickens) for dogs and cats. When you have a neighbor's dog trying to get into your chicken run - you call your local animal control. That is where those fees go. When I owned a dog, I had it licensed so when it broke loose and ran amok, I would get a phone call to come pick it up.
I don't agree with adding them for chickens, but I know in some districts, where local citizens have lobbied for the rights to have backyard chickens, the addition of these fees were what 'tipped the scale' to allow them within city limits.
"The fee you pay for your Dog License and license renewal keeps your city's animal shelter going. It is one of the primary sources of revenue for Animal Care and Control, so it can continue to provide its unique services all citizens, from finding new homes for unclaimed or surrendered pets to keeping neighborhoods safe from aggressive dogs, from caring for animals whose owners have died to teaching good pet care to school kids."