mpeg -i input.mov -vcodec copy -acodec copy output.mp4

and to rotate it to 90 degress you actually need to say rotate=0,

ffmpeg -i IMG_0864.MOV -c copy -metadata:s:v:0 rotate=0 IMG_0864.mp4

refs.

this produces a file that is as big as the original one (far too large) hence,

ffmpeg -i input.mov -acodec libvorbis -aq 6 -vcodec libx264 output.mkv

with rotation,

ffmpeg -i input.mov -acodec libvorbis -aq 6 -vcodec libx264 -metadata:s:v:0 rotate=0 output.mkv