Maybe it is because the max speed of any computer kind of reached a ceiling the last few years. Geekbench +/- 14000-15000 is the limit (off course, you have some out of this world 12 core NewMacPro's with similar out of this world prices). So people choose now: old MacPro with everything IN the box at half price, or full price with lots of desk clutter.
But it is largely emotion that sets the price. A Mini offers more for less, and when you start shopping in the Windows camp, you get the same for maybe a third of the price.
MacPro 2009 2.66 quad vs Mac Mini 2.3 i7
GB: 8034 vs GB 11639 (45% faster)
Sata 2 vs Sata 3
Passmark 310 vs 456 (3D performance 47% better, more modern shaders)
USB2 vs USB3,TB
1066mhz ram vs 1600mhz
45nm vs 22nm (4 times as cold, low energy)
The MP might feel faster on boot cause the mini has a 5400rpm drive. If you make that raid 0 SSD, the mini has NewMacPro disk speeds of 1GB/s read/write.