RVDT:
A similar question could be asked about the increased weight KingAir. The short answer is that Part 29 introduces a large number of things in the realms of failure effects analysis, system safety requirements and so on that are more relevant to aircraft carrying large numbers of passengers.
Check the difference between 27.1309 and 29.1309 to begin to see the differences. And that is just one of the very subtle, but very expensive deltas.