Doesn't Air Force One carry all kinds of defensive systems just in case? It also has to be the command plane during a national emergency, so it's got all kinds of equipment and is more heavily armored than the typical airliner. Couldn't they also send escort planes and possibly scan/search the area around the flight path? I can't imagine them leaving Air Force One alone and vulnerable like that, even if it was painted in funny colors.
As for standard airliners, I've wondered the same question myself. I've looked up and saw airliners after taking off from the airport. I don't know what terrorists actually would do, but as for what they could do, anything is possible. Could they take out an airliner with a Stinger missile? I'm not sure. But how much do Stinger missiles cost? The more budget-minded terrorists might seek out cheaper options.