I suspect the long history of the US Army here is a big factor. Redstone was here for decades before they brought in von Braun's team, which spent a year or two in TX (IIRC) first. They have test stands big enough for the Shuttle and, I suspect, for the new big boosters as well. The Space Shuttle was actually lifted by a crane onto the test stand for firing, dangling from a hook in its nose. We hear them test-firing engines occasionally, but no idea exactly what's going on out there. There's also a fair amount of "undeveloped" land on the base, which might simplify the planning and paperwork for new facilities.
Basically, there's already a fully functioning military base here, and a lot of people who move back and forth between NASA and the military. Defense/Aerospace contractors are the biggest companies in the area. Oh, and there's a river port in nearby Decatur where rocket components are shipped upriver from MS. I kind of doubt the hardware capabilities are as important as the organizational infrastructure and available personnel, however.
Don't really see the Space Command being a good idea, but there are probably fewer better places to put it -- although I would have thought whoever voted for CO would have wanted the whole works kept inside Cheyenne Mtn, for "hardening". 
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