How to install certificates with Mono on Rootless El Capitan
Although this post is quite old, maybe an answer is still helpful.

Mono's new cert-sync might help:
http://www.mono-project.com/docs/about-mono/releases/3.12.0/#cert-sync


  Mono users on Linux no longer need to run mozroots to get SSL working. A new command, cert-sync, has been added to this release, which synchronizes the Mono SSL certificate store against your OS certificate store
  
  If you want to invoke the tool manually (e.g. you installed via make install, not packages) use
  cert-sync /path/to/ca-bundle.crt
  
  On Debian systems, that’s
  cert-sync /etc/ssl/certs/ca-certificates.crt
  
  and on Red Hat derivatives it’s
  cert-sync /etc/pki/tls/certs/ca-bundle.crt
  
  Your distribution might use a different path, if it’s not derived from one of those.