Let's Encrypt is a non-profit service and we don't use your data for our benefit. We work hard to collect and retain as little of your data as possible.
We do not require you to run software from us on your server. You can use any client you want. In fact, we don't even produce client software -- all Let's Encrypt clients are built and maintained by our community (the client we often recommend, Certbot, is an EFF project).
If you don't like Certbot, we definitely encourage you to use one of the many other implementations:
https://community.letsencrypt.org/t/list-of-client-implement...
Some of these are much lighter weight than Certbot and have many fewer dependencies. You can also take your pick of what language they are written in and how they are installed on your system.
You're also welcome to write your own client that speaks the ACME protocol. Let's Encrypt is near to rolling out an API endpoint that will speak the IETF-standardized version of ACME, developed through an open standards process and in consultation with other implementers.
I know that some people have said they don't like running a large new application as root, even when it's open source. So, please have a look at some of the other clients and see if one of them strikes your fancy!
Let's Encrypt's operational funding is thanks to these entities
https://letsencrypt.org/sponsors/
which view the service as worthwhile and important and have chosen to donate funds to support its operation. The organization is overseen by these people
In this model there is no need to charge users for certificates or try to indirectly monetize the use of the service, although users are very welcome to donate if they find the service useful, and Let's Encrypt may be more sustainable if some users choose to do so.
Certbot could be configured to run without root with little effort, at least the part exposed to the web that was my concern.
letsencrypt doesn't require you to run anything on your server.
But the issue here is what is "reputable". Most of (all?) the major commercial suppliers that I am aware of have been involved in major incidents.
The only reputable supplier I could name, is LE.
But I personally like the fact there's much less commercial pressure on LE - for the time being at least.