There are a number of reasons why around 700 people die each year in aircraft operating under Part 91 and Part 135, while Part 121 operations sometimes go an entire year without any fatalities. Airlines have stricter regulations, and operations manuals spell out every nuance of how a flight and the entire airline will be run. When they do have an accident, the flight data recorder and cockpit voice recorder usually allow the NTSB to get a pretty good idea of what led to that accident, allowing everyone to learn from that accident and avoid the same thing in the future.
Part 121 operations have one other advantage that a lot of general aviation pilots may not be aware of. All major carriers now have a Flight Operations Quality Assurance (FOQA) program that analyzes the data from the flight data recorders to look for operational trends that might lead to an accident in the future if not corrected. FOQA programs got started in Europe in the mid-1970s when airlines realized there was a wealth of information on flight data recorders that could be utilized to enhance the safety and effectiveness of their flight operations.
