A craft mounted on top would also not have had to carry along the main engines for the whole trip. To meet the reusability goal this would have required some sort of system for recovering a propulsion module, either fly-back or splash-down or whatever. That would have introduced its own problems, but even so, it would be nice not to have to carry them to orbit. That's a lot of extra mass to have to slow down when the vehicle reenters, mass to increase the lift required for during the glide phase, more mass on the landing gear, etc.

Of course, even the side-mounted approach doesn't require engines on the vehicle; Buran didn't, though the Energia engines weren't reusable.

And to NIck's correct cross-range point, I would add:

the NEVER USED, mostly military, requirement for a huge cross-track landing capability