Since LetsEncrypt's API protocol is being standardized through the IETF (https://tools.ietf.org/html/draft-ietf-acme-acme), there's no reason any new competing free certificate providers can't be compatible with it. In the long term, if more show up (and I wouldn't be surprised if some existing CAs refocus their business on EV and start offering free DV certs through ACME), I see no problem with software giving the protocol a "monopoly", in the sense of building in auto-configuration support for it.