Why does compressor output 960x540 when frame size is specified "up to 1280x720"?
The original AppleTV could only playback at 1280x720 at 24fps. Because your video is at 25fps, it has to use a slightly lower resolution. If you either lower the frame rate (probably not an option) or exclude the original AppleTV, it should export at the higher resolution. I believe there's another setting than the "Most Compatible" one which excludes the older AppleTVs.