Another thing that makes Let's Encrypt possible is the very high level of automation on the server side (so that the costs from issuing more certificates stay extremely low). If you need something unusual or individualized, you simply can't get it from Let's Encrypt.
@renz1234, if you'd like to read a huge amount of history and detail about how this service came to be, you can take a look at our academic paper about this history:
But as @Osiris says, the money to run the service comes from organizational sponsors, and to a smaller extent from individual donors.
Some interesting and less-technically-detailed documents that focus on the organizational aspects are the ISRG annual reports (from the non-profit organization that operates the service):