I don't know how the TSA works at SFO, but here at BOS, the TSA checkpoint doesn't open until 4:30AM (realistically, 4:45AM because they need time to "prepare"). The lines get backed up waiting for the checkpoint to open and they back up even further when crew members have to go through screening as well (since crew members have priority).

Last summer when I flew BOS-IAD at 5:30AM, I got in line around 4:25AM and saw the line grow behind me. I was the second person in line. They let all the crew members go through the screening process first before allowing passengers to proceed. At one point, the TSA went around grabbing everyone for that 5:30 flight and letting them cut the line so that they wouldn't miss their flight.