The first, and perhaps the main difference, is the cost. You can install both on a Linux machine, and I assume that EC2 is capable of hosting both (but I don't know for sure). However, you have to pay for each FMS instance, probably making it the wrong option for EC2 with instances going up and down whenever you want. Red5 does not seem to be fully compatible with FMS. For example, right now I am evaluating both the same video player that works smoothly with FMS, will not allow me to control the search bar if the video is served with red5. However, I expect this to be resolved. FMS has additional security features (checks) SWV, which can also be useful. If I were you, I would try to do this with Red5 first and switch to FMS if you cannot get it to work.