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Part of the decision to build Mission Control in Houston was practical, the other political. Then Vice President Lyndon Johnson, who was a Texas native and former Senator of that state. Johnson knew that the new NASA programs would mean millions for his state and constituents.

The practical reason is differences in assignment for each center - Kennedy Space Center Launch Control directs the mission clock and everything associated with the mission up until the point of spacecraft launch (end of countdown). When the clock moves into a positive count, Mission Control at JSC Houston takes over the mission, and thus assumes responsibility for the duration of the mission. If it's a Shuttle, once it lands, responsibility shifts back to KSC.

It's important to understand that Mission Control is the directing center for Manned Flight training (Astronauts) and control of manned missions. The launch of the spacecraft, which is handled at Cape Canaveral Air Station or Kennedy Space Center, depending on the spacecraft being launched and the vehicle involved, and which side of the center the launch takes place at.

In other words, Houston is responsible for Manned Flight operations while manned craft are in orbit (Shuttle, ISS, etc.). Kennedy Space Center is responsible for getting the craft ready for launch and the launch itself, as well as the recovery after mission termination.

Location is also a factor - Florida typically has more inclement weather problems than Houston does (hurricanes don't usually threaten Houston), and though KSC is built to ride out a hurricane, the last thing you want is to have your key control center go down in the middle of a Manned Flight mission. Granted, in the early days of the program where space shots weren't that often it wasn't as much of a concern. But NASA always knew we'd have a long-term manned presence in space, and that started with Skylab in the 70's. As long as there are humans in space, there needs to be constant monitoring for safety and information. With the ISS permanently manned, Mission Control has taken on an even greater focus.

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