1) The ban on cell phone use is a Federal Communications Commission (FCC) regulation, not a Federal Aviation Administration (FAA) regulation. That is an important detail. The FCC did not want people using old-style analog cellular phones at altitude because their signal would reach many different towers and clog the network. The airlines had little motivation to test their planes for cell-phone interference because the phones were banned by the FCC. Now that the airlines have some such motivation (new digital phones don't have the same problem, relaxed on-the-ground rules, plans to sell in-flight cell service), the airlines seem to be finding cell phone use quite safe.
2) Most "evidence" of personal electronics causing actual interference on flights is extremely anecdotal and difficult/impossible to repeat in a lab. At one extreme, such interference may be completely myth.
At the other extreme, the probability of such interference is high enough to warrant concern when considering thousands of flights but low enough to be unlikely to impact an individual flight. This is the same logic that explains why you don't worry about getting in a car wreck going to work on Monday (low risk of an accident on a single drive), but you still wear a seatbelt, because the probability of you getting in an accident in at least one of the thousands of drives you make in your life is pretty high. Wearing a seatbelt is good insurance but "pointless" at the end of most drives. So is banning the use of cell phones if you haven't exhaustively studied their potential interference.
3) Many of the 9/11 phone calls were made from in-seat phones based on satellites and non-cellular radios, not cell phones. Using a cell phone on a plane at high altitude is difficult (sometimes/often impossible) because cell towers don't point up and don't have a range of more than a few miles. A plane at 35,000 feet (more than 5 miles up) is largely out of range of even a tower just below it. (If you're bored/daring, try turning on your phone sometime for 1-2 minutes while plane at cruising altitude. You almost certainly will not get a signal.) Once the hijacked planes were at lower altitude, cell phone use would have been easier.
Cell phones are accidentally left on onboard thousands of flights every day in the USA alone. The impact of most of these phones is simply a dead battery as the phone sucks power while searching in vain for a signal. (Many phones go into power-save mode after 15 minutes of failed searching and won't even have this problem.)