How to stop Master of Waves / Thassa decks...

The key is that Master of Waves has protection from red, not just that he cannot be targeted, meaning that damage from things like Anger of the Gods won't take him out.  It's key to distinguish this from the protection from targeting Fiendslayer Paladin enjoys.

As far as ways to deal with him, they're plentiful.  He's an easy target for any/all black removal, Essence Scatter, Banisher Priest, *insert non-red removal here*.  But the key to combating such a deck is going to be simply making sure their devotion count is low at all times.  Oddly enough this means taking out the Frostburn Weirds and Tidebinder Mages, often over worrying about Master or Thassa.  Sure, Thassa is indestructible, but really, how hard is it to keep their devotion below five?  Similarly, if Master hits the field and it's the only thing other than Thassa on their side of the board, well, they're only going to get two of the elementals.  Not a bad value to get 6 power for four, but really still not that big of a deal.

The reason I would argue the mono-blue devotion was so successful at pro-tour was because not all that many people really saw it coming.  It obviously has it's advantages over RDW and aggro for the most part, but I could easily see mono-white aggro overpowering it as well as pretty much any deck that features black and the targeted removal that affords.  Personally, I'm tossing Profit // Loss and/or Golgari Charm into the SB for any decks I'm running with black in them for the -1/-1 abilities at instant speed as it hoses not just Master, but an increasingly higher number of aggro creatures these days (Soldier of the Pantheon, Dryad Militant, Firefist Striker, Firedrinker Satyr, etc etc).

On a side note, Polukranos, World Eater offers a pretty quality answer to Master of Waves as it'll give you a 5/5 blocker who on the next turn can grow to a 6/6, pick off Master, and deal with all the tokens in one fell swoop.

I've been playing Bant Control for all of theros, and i've had zero issues with the blue devotion decks. Thassa falls to essence scatter, Master can be countered, and supreme verdict happens either the turn before or after Master or thassa can go big. Then its all down to my 5/5 stompy wurm tokens to clean up the mess. Basically, you have to play like you know what you're playing against. that means keeping your counters around for the stuff that matters, and using spot removal on the things that dont. If blue devotion is a problem in your area, build a deck that is full of removal and wraths. I also heard that Gideon, Champ of Justice was awesome against Master of waves.