It takes more than your average Estes model (man, their web site sucks!) to reach 3,000 feet. Most of them won't go nearly that high even without a payload.

Suppose this was an attempt at a homemade missile trying to down an airliner. Reaching an airliner's altitude is only part of the problem. First, you have to get really close to the plane if not actually hit it. A near hit would require a fairly large fragmentation warhead (at least a pound or two) with a proximity fuse. An actual hit would require a more accurate guidance system, probably a smaller warhead, and an impact fuse. Just hitting the plane with the model rocket without a warhead would cause very little damage.

Hitting a plane that's moving around 200-250 MPH (approximate velocity of an airliner 12 miles out from landing) with a homemade rocket isn't a trival task. Launching a rocket big enough to carry a warhead up to that altitude tends to draw attention to yourself, too. The chances that this was a deliberately hostile act seem pretty small.