It's a question of incentives. The costs of sending 100 people up instead of the normal crew of 7 and a lot of cargo on a shuttle mission would have been minimal. However, there was no real point to sending that many people into space at the same time and the risk from failure would have been insane.

So if there was some need for thousands of people to be sent into space per year then NASA could design and operate a fairly low cost per launch system. However, once they started operating highly capable but delicate system added to the fact there was little value in sending more than a token number of people into space in a given year then costs are going to spiral out of control even if the desgin was reasonable.

PS: I have even heard the argument that NASA benefited from the amount of spectacle involved in the shuttle program. If they had built something that looked and operated like a 747 nobody would have cared but build something that takes thousands of controlled explosions and then sit’s on a huge ball of fire into space and wow you must be doing something important.