Two things; first, I think there is very clever parsing of words here. The CFO specifically says not a "major" loss. That means there is possibly still some kind of loss. Remember, the PS3 sold for $600 new at launch, and even at $500 it was still costing Sony money on each console. That means that cost was very, very high relative to the sale price. Even so, they are using relatively new technology in the PS4, so they will have some extra costs of R&D compared to using an off-the-shelf AMD A10 and Radeon HD 7xxx. They likely aren't going to sell the console at cost, trying to net some of the cost/gain profit while leaving room to drop prices later as cost of production comes down.
Two, I think it would be better to have higher hardware costs as opposed to higher software costs. Ideally hardware price would be low and games would come down in price instead of go up. But there have been some quiet rumblings that game prices would be going up this generation in part to better subsidize the consoles. I rather pay an extra $50-$100 on the console than paying an extra $5-$10 per game over the life of that console. At only 2 games a year, in five years you've spent that same $50-$100 in extra costs per game, money that could have been better spent on another game.