I've had mixed experiences. Early on, I asked and was told it could stay in my bag and that's usually what I do.
I've gone through TSA screening about 20 times with my iPad in my bag and two times, they've needed to rescreen my carry on. In both cases, I had more stuff in there than normal and they said they couldn't see everything they needed to. The last time, which happed a few weeks ago, the screener said that it was because I had a bag of Trader Joe's peanut butter filled pretzels that blocked the view. On that return trip, I had everything else in my bag and had no problems with screening.
So if you travel light, you should have no problems.