To expand a bit on David Hammen's answer, the reasons for the regulations requiring FAA permits for rocket launches are related to public safety (or sometimes the egos of bureaucrats, but mostly public safety.) There are a couple of particular areas that these fall under:
Range Safety
Obviously, rockets carry a lot of fuel and often very toxic materials (e.g. hydrazine or sometimes even radioactive material for radioisotope thermoelectric generators.) Rocket launches don't always go as planned, which sometimes leads to large explosions and/or highly toxic stuff landing downrange (or just exploding on the launch site.) Thus, making sure that the risk of such an incident harming people and property is minimized is important. The FAA is the U.S. agency in charge of safety for stuff that flies, so this falls under their purview.
Aviation Safety
Spacecraft tend not to be the only vehicles flying around in the atmosphere. In general, they must share the atmosphere with aircraft, even if only very briefly. When you're flying around in your Cessna (or your Boeing, for that matter,) it's not exactly easy to see and avoid something that suddenly lights up underneath you and accelerates quickly to supersonic speeds straight up in your general direction. Thus, just as aircraft have regulations to prevent them from flying into each other, so, too, do spacecraft have regulations to prevent them from flying into aircraft.
In particular, when a rocket launch is scheduled, a Temporary Flight Restriction (TFR) will be issued telling aircraft pilots to stay away from a set boundary of airspace through which the rocket is expected to transit the atmosphere for a set period of time. A Notice to Airmen (NOTAM) will be issued to advise pilots of the TFR. Checking the current NOTAMs is part of normal preflight procedures for pilots, so this ensures that they'll be aware of the launch (assuming they actually conduct a proper preflight briefing.)
Of course, the FAA is the agency in charge of maintaining aviation safety, so this concern also falls under their area of regulatory authority (and they are the ones who issue the TFRs and NOTAMs.)
In this case, this part of the launch licensure requirement is actually useful to the organization launching the rocket. By getting a temporary flight restriction put in place around the launch site for the desired timeframe, they can ensure that some random guy buzzing around in his 172 isn't going to stray too close to launch site during the launch window. Launch windows are often very short (sometimes even instantaneous,) which means a launch might have to be scrubbed entirely if an airplane wondered too close to the launch site at the wrong time. Having a TFR in effect means that both pilots and air traffic controllers will be aware of the launch in advance and will plan for air traffic to avoid the area during the active time of the TFR, including the launch window.