If I transport you back in time and drop you in the middle of some cavemen and Ug decides he wants to kill you he will not hand you a club to defend yourself with first; he will simply bash your skull in. Rights are a societal concept. For example I believe that all people have the right to be treated equally. While many would agree with me, that "right" is in fact a relatively modern invention.
Also if the Constitution simply codified natural rights and the right to own a gun was an extension of the right to self defense then gun laws today would be much more strict. There are many legal firearms today that are obviously meant to serve a much more offensive purpose. The whole Bill of Rights was designed with one purpose in mind - to keep government tyranny in check.
As for your idea that guns are the best self-defense tool, read this: http://aje.oxfordjournals.org/content/160/10/929.full