OK, let's set the record straight here. In the early weeks of the game most players appear to have had no idea how Proton Torpedoes worked, and thus assumed they were bugged. They (probbaly) weren't, but they were somewhat confusing none-the-less.
So, to help dispell the misinformation and confusion that is still plaguing our community, here's the definitive guide on how to use Proton Torpedoes, and how they interact with missiles:
Proton Torpedoes automatically replace missiles as the weapon fired with the Right Mouse Button when aiming at heavily shielded targets (the bridge and shield generators of battlecruisers, and the communications array below space stations). However, unlike normal missiles, they take 3 (not 5) seconds to lock on. Hold your right mouse button down while continuing to aim at the target for 3 seconds, and the lockon animation will complete, transforming into a circle with 4 "arrows" pointing inward. That's your queue to fire the proton torpedo, which will one-shot the target when it hits.
At the start of a mission, your torpedo HUD will display a purple icon and "3" next to the familiar missile HUD. The purple icon indicates that you have a torpedo in the tube (just like the orange missile icons which indicate 4 missiles are loaded), while the "3" means you have 3 addditional torpedos, for a total of 4. Once you've fired 3 torpedos, your HUD will show a red "0", but the icon will still be purple. This indicates that you still have 1 torpedo left.
Once you've used all four of your torpedoes, your Right Mouse Button will revert to it's original operation of firing missiles at heavily shielded targets.
There's no need to add a toggle or alternate keybind for torpedoes. They are strictly better than missiles against the targets they're used for, so you'll always want to use one when you can. Once you understand the lockon mechanic, and realize that you have 4 torpedoes, everything works exactly as expected.