It's not necessarily about whether they're actually making money on those as opposed to covering their costs. Almost any successful company based around open source software (and often closed source) has a huge spread of customers sizes from the hobbyist who plays around with a few things all the way to Fortune 500 enterprises. By having a ramp up in terms of pricing it keeps folks invested in your platform. In cases where there's a big jump there's often quite a bit of hesitance to upgrade unless there's an overwhelming need.
Basically, it's aligning the success of your business to the success of your users. Most of what's offered in Gitlab Premium[1] would be of little value for a small development shop, yet if you have 5 users you're looking at $1000/yr for features that are unlikely to be used. It just doesn't make sense.
[1] https://about.gitlab.com/pricing/