A lot of these ships are being attacked because they are going too slow in order to save fuel, which keeps them in pirate waters for too long. They also are not far enough offshore to be out of their reach (again, because of the fuel expense). As far as arming the crews, not likely. Most of these ships have crews made up of many third world nationalities, most of which have never held a weapon in their life and few which even speak a common language.

For effective protection you need professionals, probably a dozen men per ship, armed with rifles and machine guns and RPGs, (nothing fancy or high-tech) operating under some kind of semi-official government sanction, carrying official papers and wearing uniforms (otherwise the pirates will adopt the disguise). These men will have to be trained, perhaps ex-military, and they will have to drill constantly, even though they will very rarely be called upon to fight. This will be expensive, and even though the major shipping companies and nations may spring for it, most of the flag of convenience tramps will not. It will cost more to pay and train the guard force than the rest of the crew earns.

American ships are few and far between, the only reason we have even the tiny merchant marine we do is because US law requires US flag vessels carry cargo between US ports. The Maersk Alabama was out there because she was chartered to carry US war materiel to the middle east. The Navy cannot long afford to mount a pirate patrol to protect other nation's ships, or ships that belong to no nation, but are part of some anonymous shipping company. And as long as the Navy is there, those companies will not spring for security costs. The same goes for other Navies currently operating with the US in that area. So far I've heard of Indian, Chinese, French and Russian ships out there, but as far as I know, only the US has a support capability and a fleet train operating there, and bases nearby.

The pirates are at a choke point, there is a lot of shipping is going in and out of the mideast now, what with several wars going on, oil coming out, and goods going into the gulf states.

Sure, the pirates can be stopped, but the sad truth is no one wants to pay for it. And the pirates know it.