Wouldn't the Ent D also blow up on the astroid and destroy it too? I'm pretty sure that the enterprise has a lot of antimatter on it in the warp core.

Only if Wesley is told there is no room in the escape pod.

remember that comets don't just explode Comets do not carry explosive warheads. When they say X comet hit with the energy of y many atom bombs, that's the kinetic energy released when a comet strikes a planet. That all depends on the closing velocity between the comet and the planet (i.e. if the comet and the planet are going towards each other, the speeds of the two objects add together, whereas if they were going the same direction, the speeds subtract) as well as the mass of both objects

I should mention that comets and asteroids, like the one that hit Siberia the other day, can explode on reentry, but that's because of the density of the atmosphere, gas pockets, reentry heating and all sorts of other physics, it wouldn't happen randomly in deep space.

An encounter between a starship and a comet is a completely different matter. Firstly they could just move out of its way, because comets are big, relatively slow and easy to track or predict because they follow orbital paths, they don't move randomly. Secondly, since they are slow and predictable, a ship could match the comets speed, even fly in formation with it. a collision at a relatively slow velocity wouldn't do nearly as much damage as a planetary impact. It might just get a bump. Although, as they mentioned above, if you set your ship in front of the thing and hit the brakes you'll get splattered all over the front of the comet, because again, like a planetary collision, there is a high impact velocity. However you still would not get a multi megaton explosion (except maybe from the warp core). Also, since comets are mostly ice, you could probably melt it easily with phasers, or deflect it with the main deflector before it hit. Even if god forbid you can't melt the whole thing with phasers, deflect it or fly out of the way, you could redirect it by melting the ice with a phaser beam to create a vapor jet. Scientists are already investigating this tactic against comets, an outgassing in the right spot would impart force, just like a rocket engine, and nudge it out of the way.

You hit the Enterprise with a comet and you'll have a comet with 5 million tons of metal confetti on one side of it. The shields would give Data just enough time to say Oh Sh...

Energy of the Tunguska event was at the very least 10 Petajoules (10,000,000,000,000,000 Joules). According to a few sources, the Ent D's shields operated at a power of around 4 Gigawatts (4,000,000,000 Joules/sec). Even on a huge scale, the energy flux upon the shields from such an impact would be enormous, way beyond the Enterprise's capacity.

I'm pretty sure the Enterprise-D, if the shields were so poor (kinda like in this game! HINT HINT CRYPTIC), the crushing of the ship would destroy it faster than the fuel reserves would detonate.

Also, the warp reactor itself doesn't contain most of the antimatter, it is merely a fancy shell around deuterium and antimatter colliding through a dilithium refining crystal. The antimatter pods on the lowest decks of the ship (deck 42, exactly) would be the ones to lose electromagnetic containment and react with the normal matter that comprises most of the ship.