The shuttle required refurbishments on the thermal protection system. Every single one had to be inspected. The engines also required refurbishment. The boost

The shuttle required refurbishments on the thermal protection system. Every single one had to be inspected. The engines also required refurbishment. The boosters had to be fished out of the ocean. Those same boosters that used solid fuel and that could not (and cannot) be shutdown in case of issues. And the Shuttle happened to have two of them, with a decent moment arm on each, so a solid booster failure (even a partial one, with less thrust than expected) meant a mission failure. They had to be highly scrutinized. Given that the Shuttle was also a jobs program, they were built in segments, to allow for transport across long distances. So the o-ring seals were also problematic. All in all, the Shuttle was very brittle. If they could have been mass-produced, it would have probably been more economical to just throw them away on every flight and rely on economies of scale. At least, that way, one would only have to account for manufacturing issues, not every conceivable stress that could happen during a mission.