When you control the medium of delivery and have a virtual monopoly in that market, of course Valve can afford to do whatever they want with Portal 2. Heck, Portal was given away for free many times and yet it still made $20 million.
The reason for EA and other publishers starting to put restrictions on steam is that valve and steam is a competitor and like it or not, they don't want to be giving more money to the competitor unless they can get more profit out of it
This would hold true except for recently released info that 3rd party developers see a much large share of revenue from steam than retail. About 70% vs 30%. So publishing on Steam yields much higher profit margins.