No, they aren’t giving the phones away for free, but I bet the cost of how much they sell the phones are determined by how much they are making off the store as well.
You could argue that currently Apple is using heavy in-app spenders to subsidize the cost of the iPhone for "normal" users who don't buy a lot of apps. If that's no longer feasible, then the price of everyone's iPhone goes up.
I suspect not enough developers/users will take advantage of this for that to matter, but it is a definite possibility. The idea that allowing this is just magically going to result in all positives and the only negatives are going to be born by Apple (and they already make enough money, so who cares!) is not going to survive contact with reality. The only question is whether people will make the connection (spoiler alert: they won't).