When you enable the .mov recognition in media filter it also turns on detection for files with mp4, m4v and m4a suffixes. It rewrites an mov, m4v, or mp4 link into some markup to load the video using quicktime plugin using an object tag.
This works for me using moodle using safari on iphone. But only on suitably sized video files, which are 640x480 or smaller.
It looks like mobile safari on ipod / iphone inspects the actual video file to determine if it is playable, and whether it is playable appears to depend on resolution and filetype. It may also depend on bitrate and network connection type - whether the device is connected via wifi, 3g or 2g phone network.
Watch on iphone - when it is given an html5 <video> tag or a quicktime <object> tag, a quicktime placeholder appears, and then a short time later either the play icon or unplayable icon appears in the centre of the video placeholder.
To make files viewable on ipod or iphone it looks like the resolution needs to be 640x480 or smaller. Perhaps you could think about provide alternate encoding - large size and bit rate for desktop and 320x240 and reduced bitrate for mobile version.
Here's how we do such links on our moodle site. We send the full version as h.264 encoded mpeg4 file using extra flv suffix to cause it to load in flash player instead of quicktime, and provide plain links to video files for alternate versions.
[a href="video-mobile.mp4?nolink"]video-mobile.mp4[/a] (ipod/iphone over 3g)
[a href="video-small.mp4?nolink"]video-small.mp4[/a] (ipod / iphone over wifi)
Apple recommend two alternate versions of a video - with moderate bitrate for wifi, and very low bitrate for video playback over 3G.
Here are some the official notes from apple on the limitations for video in mobile safari:
Hope this helps