The problem is twofold.
Firstly Apple. They achieved unbelievable lockin (even accounting for jailbreaking) with the App Store and are certainly raking in a fortune with it. Im not surprised Palm want a portion of the pie.
Secondly; I bet you the Pre is "sold" at a loss. Because Palm looked at the App Store and thought "hey that is a limitless pot of money, lets do it!". Im sure the Iphone/Ipod Touch is sold for the same sort of "loss" - the profit is from tertiary services (this is a fairly standard model, right).
We already have a dangerous simile for this sort of loss leader system: it's called printed news media. They make money off of advertising revenue and that is falling apart as things evolve.
There will be a revolution in phone software at some point; a time when phone providers finally realise they should open up their phones to other OS's the same way computers are. When that happens these companies are fucked; and I dont think it can be too far away. The number of disgruntled App store devs is growing, Android is increasing in popularity and gaining market traction (though I dont rate any of the production phones yet) and it looks like Palm devs will be joining the pool. That is a dangerous group of people :D