I was wondering if there is any downsides from using rvm in a production server. What should I prefer, rvm or native installation and why?
Compile your own Ruby and MongoDB, PostgreSQL, MySQL, redis, and whatever other supporting tools you rely on. This way get full control over the versions used everywhere and you can apply any necessary security or bug fix upgrades at will without having to wait for your OS vendor to supply system updates and patches. Compiling your own also makes it easier to ensure that your development, staging, and production environments are all using the same versions of everything you need.
If using RVM makes it easier for you to build your own toolchain then use RVM. In any case, using the system supplied tools often leaves you a few versions behind and leaves you hanging when you need to apply critical patches.