I would be wary of converting your video this way until we know for sure what codec specifics Apple's 720p will have. All video encoders had to be updated back in September to encode Apple's h.264 480p. Apple's site says the Apple TV will play 720p h.264 Progressive Main Profile. Nobody knows what that "Progressive" part means.
Progressive... that would be what the "p" in "720p" stands for.
Progressive Main Profile refers to 720p... that is, 1280 x 720 in progressive frames as opposed to interlaced frames. Apple I believe chose 24 progressive fps but the format can support up to 720p/63 at 50Mbps. "Main Profile" is the mainstream consumer profile for broadcast and storage applications. It allows interlaced frame coding (e.g. 480i, 1080i) but doesn't feature flexible macroblock coding and is limited to 8-bit depth. It is a 4:2:0 chroma compression format, and doesn't support 4:2:2 or 4:4:4 chroma compression.