There are settings to ignore the fact that it's rooted in AVG. I use it too, and I also have to turn off its "Real-time scanner" or whatever, cause it slows down the phone so dang much.
AVG only bothered me one time about being rooted, and hasn't since then.
But really you don't need an antivirus anyway! I do dev work with mine and install some pretty questionable things sometimes, so I like to have it just in case. I haven't come across an android virus yet, though.