Flushing rarely ever wakes me up.....it's finding my way to the bathroom in the dark that's the biggest problem; stubbing a toe on the footboard of the bed will wake you up quick!
I read that the only thing that will keep you awake once you get up in the middle of the night are lights. I generally go to the bathroom most nights at 2am or so (sorry if that's TMI). I don't turn on any lights, always flush and am back to sleep within 5 minutes.