I don't think many intentionally lose money on gas though. If they weren't covering the cost of the gas, they would raise the price, which seems like a rational thing to do for a popular game.

Quite a few do intentionally lose money on the gas itself, but it depends on the circumstances for the particular station. They consider the gas a loss leader. People are very price-conscious when it comes to gas and will drive far out out of their way to save a couple of pennies. Very few gas stations can afford to price their gas higher than other gas stations, and there is very often a price war going on between stations.

But even the ones who don't lose money are nearly always only breaking even on the gas.

It's a lot like how movies theaters make basically nothing from the ticket sales for the movie. They make their money at the concession stand.