Hosts have been asking for a pet fee since before 2012, when I started, so I think the answer to your last question is no, @Joshua495 .
By negative mark do you mean will you go down in the search rankings because you request money frequently? I don't think so, since many hosts do it, but I haven't tried it.
What I do is just make sure my nightly rate covers cleaning up after muddy dogs. Sure, that means everyone, even those not fortunate enough to travel with a muddy dog, have to pay the price, but it is easier for me.
The dogless guests don't even know. 🙂