Probably because the threat surface of a cruise missile is similar to a low-flying manned aircraft. There's lots of civilian use cases for GPS under those same conditions, where there's relatively fewer uses for speeds and altitudes in excess of the COCOM limits.

I take it it’s much easier to get rid of cruise missile than ICBM?

I just had a very dark thought suppose a nefarious entity got hold of starship, added a multi ton nuclear payload and sent it towards some city center.

How does it get prevented?

The basic idea of missile defense is to intercept the incoming missile with another missile. What really matters is detection with enough time to react and fire those intercepting missiles. There are both cruise and ballistic missiles that can travel at hypersonic speeds which drastically reduce the viable interception window. Cruise missiles are actually scarier to modern militaries, in part because they are harder to detect separately from other aircraft.

>enough time to react and fire You mention the intercept window, but it's more complex than interceptable / not interceptable, and time is not the only factor at play.

It's much easier to intercept the missile earlier rather than later, even if the window allows for a later intercept.

It's easiest during ascent phase, because: 1) the rocket is still accelerating (slower target), 2) the rocket is still burning (bright target) 3) before the payload(s) has separated from the booster (big target) 4) before warheads and decoys deploy (single target)

There are some other aspects to consider as well, like a trajectory-changing near-miss during early ascent will have a much greater impact than the same in late ascent, (depending a lot on the target type).

Which is why US missile defense began as an entirely ship based program, to be deployed where ascent interception would be possible.

Although this has changed a great deal since then; technical abilities and limits revealed through testing, as well as political/ budget constraints have shifted the tactical role of the system more state-side, not without controversy.

There are no hypersonic cruise missiles. There are cruise missiles that are supersonic for at least part of their trajectory, though that is often achieved by using a final ballistic trajectory.

And no, cruise missiles are not scarier than ballistic missiles. There is no difficulty detecting them or distinguishing them from other aircraft. Ballistic missiles are far harder to deal with because the time to intercept is tiny and they have gravity on their side.