How do hackers hack stuff!?

I just don't get it, anywhere you can read how hackers are apearantly able to hijack dns servers, edit your .httpd file and read out your entire mysql database without a password... But then HOW do they do that? I can't protect myself against it if i don't know what exactly goes on now can i? It can't be a load of magic, there must be a way for even me to understand it... So really what OS what tools and what code are they using?!