If you encode a video into mpeg4 format, even using a commercial tool whose makers pays mpeg4 license, that license doesn't extend to the resulting video.
If you post such video on your website, you're violating mpeg4 patents and have to pay mpeg4 licensing fee (up to $5 million/year).
That basically puts mpeg4 out of reach for 99.9% content creators that cannot afford even talking to mpeg4 consortium about the license.
Not to mention that most people don't use commercial tools. We use ffmpeg/x264, which is not only free but has better quality than expensive commercial tools. Even using those tools without paying a license is not permitted (although, obviously, most people simply don't understand that or willfully ignore banking that mpeg4 la won't sue them).
Microsoft and Apple pays so that users of their software can CONSUME mpeg4 format.
All CREATORS are left out in cold and have to license the patents.
Given that video becomes more and more ubiquitous, it's not an acceptable situation for the web just as it wasn't acceptable to have to pay for using .gif format to post a picture on your website (http://www.gnu.org/philosophy/gif.html)