It's the classic "grow the pie" strategy - if you create more customers that feed into using your service, it's worth it even if you're running a modest loss.
Think of it as a marketing or business development strategy, rather than a service of its own.
And such a great business development strategy at that. It's a win/win for everyone involved. Other online payment providers didn't have the foresight to create Atlas, and it's a testament to Stripe's brainpower that they had this idea and pulled it off so well.
I just noticed that their vision is to "build the economic infrastructure for the internet." That's ambitious. I wouldn't have guessed, from that vision, that they'd build Atlas. But in hindsight, it makes a lot of sense.
Think of it as a marketing or business development strategy, rather than a service of its own.