It is cheaper for them to fly you direct than through connections, everything else being equal(especially how full the flights are).
Airline pricing is ridiculously complicated, and adversarial with both the customers and the other airlines. They try to set prices wherever they think they’ll make the most profit, and showing a more expensive option that’s worse may make you feel better about the value of that $300 flight, even though they’re making a healthy profit on it. They’re still willing to sell you a ticket for a less direct route, but they’re not going to give up making a profit off you.
It also might be that the 3 layover option is from an airline that doesn’t have a direct route.
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