Why not is the important question?
Well, for one thing, major USP for the Pro is the ability to fit a range of specialist graphics cards, so they'd need a
range of graphics cards that supported Thunderbolt (not sure how that works - I presume that either the thunderbolt controller would have to be on the card, or the card would need an internal DisplayPort output with a flying lead to the TB controller on the motherboard).
It would also cut down on form factor by replacing FireWire 400/800 and other hardware that Thunderbolt speeds kill.
A lot of Mac Pro users will also want those legacy ports - for example, some video shops use 500G external FireWire drives like floppy discs, there are FireWire audio devices.
Secondly, a lot of the form factor is to do with having
internal PCIe slots and
internal SATA hard drive bays. One thing Thunderbolt
doesn't kill is 'proper' PCIe and SATA, and the convenience/neatness of having everything installed inside the PC.
A form factor the size of the ill fated cube, 2-3 internal SATA III bays, 2-3 PCIe slots, USB 3.0, Xeon or Core i7 processors,
No, that's not the form factor of a Mac Cube - that's the form factor of the TARDIS. I suggest that you get a couple of 2TB 3.5" HDs, a pair of full-length, high-end graphics cards and a ruler and c.f. the dimensions of a Mac Cube. (Don't forget the space for a pair of Xeons and the requisite cooling).
RAM, and either an external graphics box or PCIe card.
...which would have lower bandwidth than an internal 16-lane PCIe bus.
bidirectional cable to displays
...bidirectional cable to the 1 (one) Thunderbolt display currently available, which, while very nice, is really a 'pro-sumer' device c.f. the huge range of specialist graphics pro displays that can connect to a Mac Pro.
Sniping aside - I wouldn't be surprised if the "Mac Mini Pro" concept does emerge - the appeal of Thunderbolt is that it can give small-form-factor systems much (but not all) of the expandability of a full-size PC, and as the power of SFF devices increases, the number of people who actually need a "Mac Pro"-like machine is drastically reducing, so Apple would probably shift far more "Mini Pros" than they would Pros. However, I guarantee a great wailing and gnashing of teeth from current "Pro" customers if they do.
Its not that Thunderbolt wouldn't be useful at all on a Mac Pro - its just not a priority when the Pro already has cheaper/faster ways of achieving the same effect.