Apple's not doing this for the money. This market is barely on their radar in terms of revenue.
I don't believe that's true; okay so custom fabrication of some parts isn't going to come cheap, nor is the R&D, but the markup on Mac Pros has always been pretty high, even though they offer decent value for money, as Apple can get the parts (relatively) cheaply.
Also, the factories in the US are bound to be used for other machines in future, maybe we'll see redesigned Mac Minis coming out of them soon? They also seem to be largely for assembly, with maybe the cases being made there. The rest of the components still sounds like they're manufactured elsewhere. While it's a step in the right direction, it's not what I'd call "Made in the USA" personally.
Don't get me wrong, I do believe that Apple has made some great choices in the new Mac Pro, even if I wouldn't have made them myself, and there's bound to be at least two more versions of the new Mac Pro as-is, simply with upgraded components. So while development costs are going to cut down on initial profits, there is absolutely no way that Apple is making this new machine at a loss. At worst the first generation will only pull in a small profit, while the future ones will do a lot better, so in the long term they're definitely making money on them. Even after they've released several generations, its hard to see the new Mac Pro getting a lot smaller than it is now, seeing as how nearly every bulky part has been removed, so it may even endure as a design for as long as the G5 design has, with some tweaks along the way.
Granted we're not talking iPhone, or maybe even iMac, levels of profit necessarily, even with a high markup, but so long as it isn't losing money I think it's in Apple's best interests to ensure they still have a high-end option in their lineup.
Also, Apple stands to potentially make
more money from a new Mac Pro customer than an old one, as it upgrades in the same way as a Mac Mini; Time Machine backup, remove computer, swap in new one, connect drives, Time Machine restore. Okay so there
are possible upgrades for both the Mac Mini and new Mac Pro, but they're not really normal user upgrades (other than RAM), plus if you have the money to spend on a new Mac Pro for professional use, then swapping to the latest and greatest unit every year or so probably isn't a big deal, and you can recoup some of the cost from selling the previous unit.