These problems have nothing to do with root, I have a rooted EVO 3D on CleanROM 2.9.5, and run Hulu Plus fine!
Here's how to fix:
The problem you are having is that by default, CleanROM comes with an ad blocking hostfile, something that prevents Hulu from displaying ads normally, the application just won't play your video until it plays the ad.
So you must install the non-adblocking host file, which you can find in ROM updater's addon section, you must enable addons in the settings if you have not already (use the default repository). Scroll down the list until you see the non-adblocking host file, and install it by restarting into recovery and installing zip from your sdcard's cleanrom folder.
Generally the ad blocking hostfile causes more problems than it's worth. Especially with apps that have forced ads, like hulu, netflix, ect.