What are you talking about? At $399 with a component and manufacturing cost of $160, they're making almost 40% on a phone that had minimal R&D costs, and as far as I can tell, no advertising costs.
In fact this is AMAZING news as it means what I suspect will happen is more likely to now:
In 12 months when I believe Apple will release a premium 4" 7 phone for $599, the SE as is, can drop to $299 thus making it even more affordable, and maintaining the $250 differential with the 6s with which it will be depreciated alongside. Then when the 6s drops down the the $449 traditional "entry price", there's still room for the SE to drop to $199 and still make a profit, not to mention some of the parts will cost even less then ... and now we're talking iPod Touch replacement territory. If Apple can sell an iPhone for the same price as the iPod Touch, then there's no reason to keep the Touch around.
Meanwhile the "7 mini" or whatever it will be called, will depreciate with the 7 keeping a more profitable premium offering in the 4" lineup, until it too drops low enough to replace the SE.
That of course all depends on how well the SE sells. If the demand for a 4" phone doesn't materialize, then Apple could shelve its plans for annual updates. The problem is, they can't continue selling the old 5s case indefinitely. At some point they will need to update the entire hardware, and Apple doesn't do that without charging a premium, nor should they considering the R&D that goes into a new design. Which is why, no matter how well the SE does, unless Apple decides to discontinue the 4" phone altogether, they will most likely release a new 4" phone early enough in the 7 life cycle to earn back the launch costs. And one motivating reason to keep the 4" around is not only lower cost, but crossover with the dwindling iPod market, which could be discontinued entirely in two years once the A8 has outlived its usefulness.