This is hard to answer, because the contract is generally hush-hush among developers and Microsoft. But that doesn't mean we can't estimate.
Fez cost 800 XBLA points, which is $10. The game then went on to sell over 200,000 copies on XBLA, so we can guess the game made roughly over $2 Million.
Xbox may take anywhere from 30%-70% for distributive and platform fees, so if we conservatively say that it was 50/50 split, then Phil Fish made $1 Million.
But that million is from XBLA profits alone. The game is also sold on the pc platform, and they have plenty of souvenirs (t-shirts, memorabilia, etc.) which could add significant profit.
The only factor undetermined is the cost of producing the game.. Since it took five years, I'll assume that the cost was extremely high (estimating about $100-300k/year for the typical indie game developers)