You don't! Wrong game!
Oh, wait, this was done before. Dang.

You need them to lock on by holding the key.

It kinda feels as if Proton Torpedoes are a hidden way to raise mission difficulty again. But I am not sure they actually get harder. I believe the issue is more that proton torpedoes requrie a different approach to these missions. Since we "mastered" the mission without proton torpedoes, this can be very confusing.

But on the other hand - finally I can destroy those dang bridges!