Yes, I think you are missing a lot.
Although the Mac Pro looks like a nice machine to have, it still seem crazy to me to drop 4-5k on a machine that will be outperformed by a MacBook Pro or iMac a year or a year and a half later for a fraction of the price.
And that's not even considering the MBP and iMac both come with keyboard, mouse or trackpad, monitor and speakers.
I see it as you're not really paying for the power, but for having that power 1/1.5 year in advance. And it seems like people buying Mac Pros don't upgrade every year, a lot of them plan to keep theirs for like 5 years, so it doesn't make sense to me.
For the same price, you could buy the best iMac every year and resell it, and you would end up:
1) Having a more powerful machine on average
2) Paying less
3) Always having a warranty
4) Getting the cool new stuff first (Thunderbolt, 27" IPS display, FaceTime HD...)
So unless you work requires you to have power that can't be achieved with a high-end iMac/MBP right now, and that you also upgrade/change your Mac Pro every 2 years or less, I see no point in buying it.
Am I missing something?
First, the only MP comparable to the iMac is the entry level quad core machine, and that should be compared to the top end i7 iMac with the extra memory. Since the MP is easily expandable I would get memory from Crucial, and an SSD from Newegg, and a monitor from Dell - U2412 probably. This isn't completely Apples to Apples, but here is what I came up with:
Mac Pro - Quad core, 1TB HD, 4GB RAM $2,500
24GB RAM from Crucial - $325
256 Crucial SSD - $300
2 x 24" Dell U2412 IPS LED monitors - $630
Mac Pro total: $3,755
iMac - 27" i7 with extra video memory, 256GB SSD and 1TB HD - $2,899
16GB RAM from Crucial - $240
iMac total - $3,050
So for an extra $700 you get:
1 expandability - add HDs, Video card, etc.
2 more screen real estate than a single 27" screen
3 theoretically better performance for things like virtualization
4 theoretically better longevity of components when left on 24/7
But there are some cons
1 noise
2 power consumption
3 where to put the big ass tower
Bottom line - it depends on your needs. I use Macs professionally, and the ability to add a couple of HDs to the machine for redundancy, add an additional card for potentially up to 6 monitors etc is something I need. The Mac Pro is also more suitable as a "server" machine meaning I can set up shares and services for others in my office and coming in over the VPN, and leave it running 24/7.
Personally I'm watching this very closely, and I want to see the benchmarks for the new Mac Pros (assuming there are some - if there aren't it's an iMac for me) vs the new iMacs. I suspect from what I've read that the new Mac Pros will once again outperform the new iMacs. I purchase machines on an assumed 5-year active life and typically replace each machine every 4 or so years. So even at $3700, that cost amortized over the 5 year life of the machine is only $750 a year or $63 a month. vs $608/year, $51/month for the iMac. When viewed this way the additional $700 is nearly immaterial especially since it's all depreciated / expensed anyway.