Erm.... the same reason we today don't use nuclear weapons on every job that requires explosives?
This is a straw-man comparison:
In star trek, photon torpedos ARE matter-antimatter warheads - nuclear weapons, capable of destroying a planet in seconds (this was repeatedly confirmed on-screen).
Which is to say, these "explosives" can destroy a planet/can generate mega-death events as easily as transphasics.
And these photon torpedoes are NOT sufficient for engaging and destroying enemy ships - star trek shields negate to a large extent their power.
Meaning, in star trek, "explosives" - matter-antimatter warheads - don't get the job done; not with any degree of proficiency, anyway.
In other words - despite Christopher's rhetoric filled with straw-men - photon torpedos are NOT, in any way or shape, morally superior to transphasics.
And transphasics are the better tool for starship combat.
Why are they not used? No objective reason, really - if you discount straw-man filled rhetoric, that is.