It really depends on the location, but the companies like Fox, Advantage, E-Z, etc have a certain reputation. They have limited locations relative to the big players, often have off-site locations (even when there's a consolidated off-site rental center which makes it off-off-site), and have a certain reputation for finding ways to charge extra.
Yeah you get angry about long lines, but there are just so many variables that you're right that's it's unfair to take one experience as indicative of a systemic failure. They're running on pretty tight margins, so having extra staff on hand for every eventuality is going to be a money loser. I remember arriving in Vegas waiting for my family to arrive on a well delayed flight. I was supposed to pick up the car before midnight, but I chose a slightly different option because Enterprise closed from midnight to 6 AM (now apparently 1:30 to 6), but Dollar was 24 hours. When I finally met up with them and headed for the rental car center, it was maybe 5 AM and there was no line. However, the agent said that if I showed up on time the line would have been well over an hour. I might have been in trouble had a reserved with Enterprise.