It feels a little more reasonable to me than removing your shoes or restricting liquids. Even if the shoe bomber had been successful, he wouldn't have been able to take down an entire plane. But it's trivial for a rogue pilot to kill everyone on board a plane. Since 9/11, cockpit doors have been reinforced so that it's basically impossible for anyone in the cabin to force their way into the cockpit. Ensuring that there are at least two people in the cockpit isn't too much of a burden and basically eliminates that attack vector.
Maybe, but it's still trivially easy to break the system. Just slip something in your co-pilot's drink. Or knock him or the (probably female) cabin attendant out with something heavy.
It seems like it's at the same level of the rule that the pilot and co-pilot can't order the same meal at the airport before a flight in case they both get food poisoning simultaneously. Doesn't guarantee that they don't both get sick, but it's a relatively minor imposition and reduces the odds by quite a bit.
