This is on page 18 of the FMA12 CWP/PHP guide:
=== copy ===
How web users view container field objects
When you publish a database using the Web Publishing Engine, the following limitations apply to container field objects:
* Web users cannot modify or add to the contents of container fields. Web users cannot use container fields to upload objects to the database.
* For databases that use a container field with thumbnails enabled, the Web Publishing Engine downloads the full file, not a thumbnail.
=== end ===
I haven't tried, but I would imagine that you could have them upload through a web form that, when processed, saves the file in a web-accessible location, then trigger a FileMaker script to perfom a server-compatible script step
Insert from URL (Select; No dialog; tablename::containerfield; "http://domain.com/user/files/file.mov"]