Rats are fine by me as well and I also had a number of them as pets over the years. That said, the rats in San Fran that I saw a couple of years ago when visiting were HUGE and I was not a fan.

I suspect some of the fear of rats is that they generally give off the vibe of "I'll bite you if you get close" vs. the skittishness of squirrels who will scurry off up a tree if you even try to approach.