The most restrictions occur on the ground as that is where you might have to evacuate with no notice.

Therefore, they need plastic cups while taxiing because they don't want to worry about broken glass hindering an evacuation.

At 30,000 feet, glass is fine, because either:

a) you'll have time to stow things in preparation for an emergency landing.
or
b) Ummm, in the case of b, let's just say that it really doesn't so much matter about the broken glass.