We use it too. Personally, this is one of the last of my worries. Worry about being successful first – no one sues those that are unsuccessful. When you succeed and by some chance they come after you (and even that's a really remote possibility since they'd go after Red5 itself and not some site that's using it), you'll have plenty of money to license the FMS.
I work for a large company and everything that goes out the door is patented; I imagine Adobe is the same way. However, I just did a search and didn't see anything obviously relevant.<p>I have my doubts that file formats or protocols are patentable, but that won't stop the USPTO from granting them.