The word comma only means the mark ",", but why does everyone say it as a comma or commas not the comma; likewise a question mark not the question mark only indicating the mark "?".
As JR pointed out, the confusion seems to be coming from the very first statement you make:
The word comma only means the mark ","
I believe you are saying the comma is always used to refer to a specific instance of a comma. This may be true, but it doesn't preclude a comma from referring to any instance of a comma.
I think a more accurate and complete statement is this:
The word comma can mean any mark ","
This allows a comma and the comma to have separate usages and still live in peaceful harmony in the same universe.