The way my school works, we have homeroom once every other week (about) and the classes are shortened a few minutes to make room for it, and the pledge is said in homeroom on those days. Other days, it's said in first hour.
Both my homeroom teacher and first hour teacher have no problem with me sitting down. One time, though, a substitute told me to stand and I said "No". He just left it at that.
I haven't stood for the pledge in a very long time. Not really as a protest against America, but as zorm said, I've usually started doing something or another while not paying attention to the preceeding anouncements and I'm too lazy to stand up. Also, pledging alegiance to the flag is a form of idol worship, I guess, but nobody cares if I stand up or not in the first place.