Is it against the rules to fly in the NBA?

I don't believe flying would break any specific rules in the NBA (or FIBA) rulebook - but that's not really the same as saying "flying is legal in the NBA" as the governing body for a sport (any sport) isn't going to waste its time writing explicit rules to cover situations which can "never" occur.

If we ever got to a state where flying was a reasonable possibility, something would be done to the basketball rules to regulate it. For example, the rules regulate goaltending, something which is a realistic possibility for humans today.