Many HD MKV files will work in the free version, they just cannot have DTS or Dolby audio.
The Pro version of Infuse includes some technology that requires expensive licenses, and sadly ads in the free version wouldn't be enough to cover that.
I am not wanting to argue, you know better than me about licensing, but there are free apps (their UI is ugly as hell, mind you) that will play files that the free version will not. I am unsure how they get around it. I won't mention them here as my intention is not to drive sales away. AFAIK, VLC, when it was available, also handled these files just fine. On jailbroken devices, XBMC does the same.