I actually have a theory on what a dilithium crystal is.
Okay, we know that if antimatter touches any form of matter it instantly vaporizes the matter in an equal explosion.
However, dilithium seems to be the odd man out of that equation. I've pondered that for a while, and eventually stuck it in the back of my head as just a part of the show. Which it is, but I like to think so...
Well, I determined that the only way that crystal would be different if it was somehow ALTERED by being exposed to subspace, thus giving it the inherent property to phase into subspace when antimatter touched it, THUS phasing the actual plasma that is fed into the warp engines allowing it to be altered again into subspace fields using the properties of the warp coils. Perhaps asteroids that held dilithium flew through space, and occasionally these asteroids would enter a subspace pocket, to come out again with the altered dilithium. Then these asteroids would pelt a planet, littering it with dilithium. This would also explain why it was so hard to find dilithium in TOS years, because this phenomenon would be pretty rare over the eon's.
Of course we know now the Federation has obtained the ability to artificially create dilithium. But that is generally what I think the crystal is, and the reason it doesn't mutually annihilate when antimatter touches it.