While I mostly agree with your statement, the answer to this question is quite simple: The free tiers are limited in resources and they have enterprise tiers that pay for the actual service and grant you all features. You know what you are getting upfront. If Skypack will - as you suggested - throttle plans in the future (or whatever they come up with) that's not the same product anymore you started with. You most likely need to adapt your own product to this changes, which is usually paired with costs on your side. You won't have that happening on CloudFlare, Heroku or AWS. Also there are exit strategies, contracts, SLAs and so on. Something like Skypack may go offline tomorrow and that's it.

So people might just wake up one day, only to find out this service just disappeared because they ran out of money. I would say this would be bad, even for an indie developer or a small company, but any larger company wouldn't even take this risk.