Why would it?
An object outside it's natural state must return to its natural sate. As such, if the form and function of a hieracrhial system was innate knowledge (ie, in our nature) then any form of governance which is not in our nature would quickly fail. So, the process of governmental change would be evolutionary, and not something that happens in bursts through out time and space.
Changes in the natural and cultural context of human existence are much more rapid than that, and humans adapt through the use of intellect and innovation more than through biological changes
I suppose 'thousands' was a bit much, but the principle of governmental change being an evolutionary process does remain. Also, there is no human culture, so it's change throughout time is pretty much a gaurantee.
Nevertheless, humans have always organized themselves into packs of some form or another, and a ruling minority (or a single leader in the case of small groups) has always led the pack.
I do admit that there will always be leadership, but this is like with sex -- it's a constant among social creatures. Again, this (as a lose concept) is a universal, but the form and function changes, implying to me that it's not nessicarily a form of nature to have governance (which is a different then small tribe led out of fear).
base instinct is the belief in God
This is a similar technicality. While a religious beleif (which is different then the belief in God) does seem to very common, but not a universal. There are countless differenet religions, sects, cults, and personnal views, not all of which include a form of God (Buddhism being the first example that comes to mind). So, we again get into technicalities over religious beliefs as a whole vs. specifics.