Increasing the rate limit is something, if you are are large provider with a lot of domain names. Or a large organization (like an university) with a lot of subdomains.
For you, Let's Encrypt certificates are free. But for Let's Encrypt, every newly issued certificates takes its toll on the load on the LE infrastructure and adds to the total costs of the project. Please read all the documents in the future when you use a 3rd party service.
Every opensource is doing job is backed by successful organisations and without those sponsors it wouldnt have been possible. We are also providing free services that too at startup stage without any Sponsors and without complaining it.