The Mac Pro does target a group of high end users who are willing to spend an unreasonable amount of money for a computer. Even with the extra R&D it is likely that Apple would make money on a new Mac Pro, though the volume would not be high and the profits not large in absolute terms.
The biggest benefits for Apple of having a computer in that category are about forcing themselves to stretch themselves technically and about presenting an image of themselves as being a high end producer of aspirational products. The Mac Pro requires Apple to explore and solve some significant technical problems. Often those solutions can end up being applied to the lower end of the line down the road. Having an expensive but powerful top line product reinforces the image of Apple as a technical leader. Customers don't necessarily expect to buy one but they can dream of doing so and then will buy one of the less expensive models. This halo affect is common in car product lines, too. It's why VW bought Bugatti and why lots of companies have super expensive, low volume top line products that make their other products look more appealing.
