How are spacecraft and aircraft traffic coordinated?
A TFR will be issued for the area that the spacecraft is expected to need for safety. Here is an example.


  No pilots may operate an aircraft in the areas covered by this NOTAM (except as described).


No exceptions are described, and the airspace is patrolled (at least for manned launches). As with errant sea vessels, a launch may have to be scrubbed if the safety area is compromised.

The company or agency in charge of the space flight operation would need to contact the FAA to coordinate such a TFR.

For space shuttle landings, Special Use Airspace was established. The shuttle landed in a pretty steep profile, so it only spent a relatively short time in controlled airspace. ATC coordinated directly with NASA while the shuttle was transiting the airspace.