Ok, The SVN version of the game works fine. No error thrown by the input handler. No need for keys.cfg at all.
I would recommend building this baby (UQM) form SVN source rather than the 0.6.2 source package.

PS SVN checkout includes all the content as well.

...and now...on with the hacking

Well, ok I see why I can't find keys.cfg
I checked the relase notes for 0.6.0 and found that Key config is entirely in-game

Unfortunately, sc2code/libs/sdl/input.c still looks for keys.cfg and throws an error when it cannot find the file.

...so I'll try the SVN version which currently downloading (STILL *sigh*)

if not I'll patch the source and submit said patch

I'm getting the same error.  I'm building from source. I am using 0.6.2 source and the 0.6.0 content file.
(these are the files linked too from the website)

so I unzipped the content file and still no keys.cfg

is there a 0.6.2 content file? or just the 0.6.0?

right now I'm downloading from the subversion repository on sourceforge.net in hopes of finding a keys.cfg

yes everything is in the right place and the uqm wrapper script points to the correct content directory