Really depends on what part of it. There are things like offering your bus seat to someone who needs it, or waiting for people to exit before you enter. Those indeed make sense.
And then there's what the other commenters pointed out, arbitrary rules about what cutlery to use and in which hand and such.
The thing you're missing here is that a lot of people are not capable of reading the animals' body language. Hence, permit. Also the part where just taking some wild animal home as a pet isn't ok, and to actually care for one you would usually require some pretty specialized knowledge.
I also fully agree that dogs above a certain size should require permits because holy fuck I know most of them are pretty chill and at most kinda loud but they still scare the hell out of me and I can't trust their owners to control them in all cases. And while knowledge of how to handle them is more common, some people still fuck that up..