There are several disadvantages I can think of to using a railgun to launch a payload into orbit versus using a rocket or spaceplane type system.
The first, as noted by a previous poster, is that the acceleration loads will be pretty abusive, probably on the order of tens of thousands of gees (using tank/artillery shells as a base line - I realize that it will probably be gentler than the 20-60000 g’s a shell from a tank gun experiences). Many payloads will not be able to survive this. Not to mention the effect of the EM fields used to accelerate the payload.
The second concern I have is that you cannot merely accelerate the payload to escape or orbital velocity. You have to accelerate the payload such that after passing through a heck of a lot of atmosphere it has escape/orbital velocity. A space plane or rocket trajectory generally stays at relatively low velocities (Mach 3-5 ?) while in the lower atmosphere and only accelerates to orbital velocity when it reaches the upper atmosphere where there is a lot less air to generate heat and drag. If you are going to fire the projectile at M=25+ on the deck or even at a modest altitude you are going to have ridiculous heat loads and substantial drag loads (IIRC drag generally goes with Velocity²) which means you have to have its initial velocity even higher to deal with drag induced deceleration, aggravating the problem.
Does all this mean it can’t be done more economically than a rocket with a payload fraction of a few percent? I tend to think that at least in the near term future rockets and/or spaceplanes will remain the more economical.