They don't have the expertise or the manpower to fix their build system. That means it's not really feasible to use it to distribute your apk, unless it can be months out of date without any problems (such as your users complaining constantly, or things breaking, or a known exploit remaining in the client because it's impossible to push out a fix).
You can host your own repository if you so wish and have users download the app from the standard F-Droid app, similar to the many PPAs available for Ubuntu.
You end up having complete control over your APK distribution and users can receive updates through F-Droid.
F-droid certainly isn't perfect, but it's the best Play Store alternative I've seen.
You can always do everything yourself, and given that you can add repositories and the app handles it transparently that's a great alternative. That's assuming, of course, that you do have the expertise to run one. That certainly isn't true for most app developers I know, and that's logical - it's not their field.
It's definitely the best alternative, but that doesn't make it a good alternative right now.
