As I wrote in an earlier post, if the FAA decides that a vehicle designed for space tourism has to meet the same requirements as ordinary aircraft, then the certification costs would easily top $100 million. Aircraft intended to carry passengers for hire (everything from a private plane used for flight instruction through airliners) have to meet some pretty severe regulatory requirements. For example, not only the aircraft itself must be certified, but virtually everything in it such as the engines, avionics, and even the seats and uphostery. It commonly takes years and many million dollars to get even a simple 2 seat plane certified for production.

For Rutan's design, you'd have to certify both the White Knight and SS1, including the engines and avionics. At least the avionics are the same in both vehicles (White Knight can be configured to fly the same descent trajectory as SS1, making it useful for training). I don't think the FAA has any certification requirements for a rocket engine, which means they'd be figuring out the rules as they go. At the very least, you'd have to conduct many test firings until the FAA is satified the engine is safe and reliable. You might also have to build at least one static test aircraft (perhaps one each of the White Knight and SS1) for structural load testing. Most flight test programs involve multiple prototypes, with some of them sometimes tested to destruction to determine things like ultimate load limits and fatique life.

The FAA went through similar gyrations years ago when a developer tried to certify the first composite airplane (the Windecker Eagle). In the end, the certification costs were so high ($20 million then, about $97 million when adjusted for inflation) that only a handful of Eagles were ever built.

As far as licensing the glide path and things like that, I don't think there would be much of a problem since the test program has to demonstrate the vehicle's flight envelop. There could be noise restrictions (the afterburners on the White Knight are quite loud) and things like that, perhaps relating to sonic booms, but that may not be a problem out at Mojave. Edwards AFB is right next door, so the people there are probably used to sonic booms.

Now, it's also possible that the FAA would see a vehicle like the SS1 as something new and unique and so it wouldn't have to meet the same regulatory requirements as ordinary aircraft. They did so with both experimental (homebuilt) and ultralight aircraft. However, neither of those categories are allowed to carry passengers for hire except for flight training purposes. When it comes to carrying passengers for hire, I don't know of any cases where the FAA has gone for lessor regulation.

Here's a link to the FAA Certification Information webpage.