Sure, but missiles have to propel themselves, are very large compared to railgun projectiles, and are easier to break apart by putting a heavy wall of lead in the air.

Railgun projectiles have none of these disadvantages. They don't need propellant (or a warhead; the energy delivered upon impact is more than sufficient to break things without needing to explode), they're a solid projectile (and as such can't be as easily destroyed or knocked off course), and they're smaller than a missile is making them much more difficult to track.

To successfully defeat an incoming railgun projectile, it would both required sufficient detection technology coupled to a laser that would need to fully ablate it; where missiles require detection of a significantly larger object and can be defeated by shooting at them/more active protection measures.