They were flown out, but not when air travel was banned.
Firstly, civilian air traffic was allowed to resume "at 11 a.m. EDT [eastern daylight time] Thursday [13 September 2001]", so there was only about a 48 hour period where flights were prohibited.
As explained in a 30 September 2001 New York Times article:
> Both planes, one jumbo jet carrying 100 family members, and the other 40, were eventually allowed to leave when airports reopened and passports were checked
...
> The young members of the bin Laden clan were driven or flown under F.B.I. supervision to a secret assembly point in Texas and then to Washington from where they left the country on a private charter plane when airports reopened three days after the attacks.