Applying companion customizations

You need to go to a private place, such as your ship or a cantina.

From http://www.swtor.com/community/showthread.php?p=1200623:

To fire a proton torpedo, position your cursor over the target and hold down the right mouse button until it establishes a lock. Your cursor must remain over the target the entire time. Once it's locked on, release the right mouse button to fire the proton torpedo.

This is different from regular missiles where you can just single click or drag over top without remaining over the target.

Edit: After obtaining and using them, I can verify that Killer's answer is also somewhat correct. They are only usable on "heavily shielded" targets: those that would normally take 4+ missiles (in the harder missions), such as the target on the bottom of space stations and all 5 shielded targets on Super Star Destroyers (or whatever the larger frigates are called). The shields on the smaller ships can't be targeted with the torpedoes.

Note that I said 5 above — Killer's assertion that there are never more than 4 targets you can use the torpedoes on is incorrect, especially since there is more than one ultra-ship in some missions. The (now deleted) answer he quotes was actually also correct — you can't use regular missiles on a heavily-shielded target unless (a) you are out of proton torpedoes or (b) you have fired a torpedo and it has not yet hit its target.