It's valid to discount the Mini because when you buy a Mini you are paying for several very significant features that are lacking from a typical desktop. If you want to make a fair comparison to the Mini, look at home-theater PCs that will be similarly small and quiet.
The mini, by virtue of using low-power laptop chips and other techniques to reduce its size and power consumption, will always have a higher cost than a budget tower with equivalent clock speeds but a 250W power supply built by the lowest bidder, loud fans, and other commodity parts.
If all you are looking for is a cheap tower machine built from commodity parts, any of Apple's offerings will require you to pay a significant amount for features that you don't want, because the Apple machine isn't meant to be a generic box or to compete with generic boxes. The Mac mini, iMac, and Mac Pro all target niches that are different from the low-budget, ultra-low-margin desktop market.
It's really no different from saying that the MacBook Pro is an overpriced desktop - of course it is, because it is more than just a desktop. Apple doesn't make ordinary desktops, much to the consternation of almost every hacker who wants an ordinary desktop (but not a workstation) with a good unix-like OS. If Apple did make a generic ATX form-factor box, nobody would take exception to the idea that the Mini, iMac, and Mac Pro are in different categories.
