CI in a Linux environment setup

>>> But my routes only contain one line, I was referring to that I have already tried setting it up to 'welcome' and nothing, right now tried setting 'welcome' and the .htaccess you provide me and still nothing.

Nothing??? Did you check the error logs?

>>> EDIT: So I have set up some old projects I had withing htdocs folder containing only, HTML, CSS, Bootstrap and some jQuery and they're rendering ok, seems it's problem within CI.

OK - in the project that is not working, please point the system directory to the old projects that are working OK and try and get the Welcome_message to display.