It isn't unthinkable that the 3DS sales have simply been better. From Beril's Gunman Clive sales thread:
The fact that Android sales are massively outpacing iOS sales on a similar curve to the 3DS vs. Steam situation indicates the effect we're looking at here. When you have a platform that's under-adopted and as a result under-supported, titles that are solid but wouldn't necessarily be absolute top-tier can flourish as people try to weed through crap. We saw this with retail games on Gamecube (look at how well totally random stuff like Tales of Symphonia did in the US) and we see it now with some DD shops.
The Wii U and 3DS are definitely experiencing a bit of this. There isn't as much support as Steam or XBLA/PSN, but as a result titles that would be second or third tier elsewhere can get a chance. Trine 2 is much easier to promote on Wii U (where it's a polished, well-constructed title that many people will enjoy) than on Steam (where it's a title that's mostly just not quite as good as some of the other similar options.)
This is a very real phenomenon, and it's absolutely worthwhile for indies to pay attention to this as a possible factor in their platform decisions, but it doesn't really scale up. You could do this with retail games in 2003, but nowadays even really big games don't sell well at retail (and the Wii U itself doesn't sell well enough to provide the needed install base.)
As stated above, Sony did make a lot of profit during the PS1 and PS2 days, and probably squandered all of that away during PS3.
This isn't a reasonable method for evaluating a company's profitability. You don't just add up numbers from the beginning of time and say "oh, in this entire field of business they're profitable or not." That'd be like counting sports team records from the time they were founded -- it has the result of making current operations increasingly unimportant to the totals, and it doesn't reflect the actual reality of the operating business.
You have to compare distinct periods of time, either a yearly basis (what shareholders use as a reasonable strategic chunk) or per-project basis (with something like a console, you amortize it so that costs are upfront and lead to profit later -- so it's reasonable to analyze a single cycle as a whole.) By either of these methodologies, both Sony and Microsoft have had periods of profitability.