That's because this synonymousity (is that a word?) was co-opted from a different definition of "hacker" (i.e. in the "Jargon File" sense of "someone who demonstrates creative ingenuity"); in that sense, having the freedom to tinker with things is strongly desirable to someone possessing the "hacker ethic".

'Tis one of the side-effects of the term "hacker" having multiple meanings, for better or (in my opinion) worse.