Apple did pay---Straight from the WSJ:
‘Songs of Innocence’—and Commercial Experience - Speakeasy - WSJ
“We’re not going in for the free music around here,” Bono joked on stage. Apple didn’t pay a traditional wholesale price for each of the 500 million albums. Instead the company paid...
I am not going to go as far as say they are not out to make money--they are just being smarter about where they expect those funds to come from....This is a win win situation
Actually they made it quite clear that they are not into free music either--Apple paid them to have it up on itunes until the physical release in October.