minify html, css and js on nginx

The way you have it is actually correct, the issue that you are having is likely the same one I am (and I'm not sure why it is) but basically it comes down to NGINX's rewrite rules ignoring the ? next to the $1 in the rule.

A work around for this is simply instead of going to example.com/min/f=path/to/file.css just put a ? in front of the f example.com/min/?f=path/to/file.css.

A better method would be to just serve the files as a group:

For the best performance you can serve these files as a pre-defined group with a URI like: /min/g=keyName

To do this, add a line like this to /min/groupsConfig.php:

return array(    'keyName' => array('//path/to/js/file.js', '//path/to/js/otherfile.js'));

Chances are though, you may need to use /min/?g=keyName.

As a side note, minifying and bundling isn't just ~1kb it can (and tends to be) much more. It has a huge impact on the user (especially on mobile devices). A browser can make 6 concurrent connections, so if you have any more files than that being downloaded, the user is waiting for them, one of the projects I recently have been working on had roughly 60 requests being made for different js and css files (the original coders were... all inclusive in the plugins department). The entire page was roughly 1 Meg and took 3 seconds to download uncached (nothing was cached, because the previous coders don't understand caching). I minified bundled and compressed everything into 3 files (removed the useless stuff too) and got the entire page down to 20kb uncached, 3kb cached, with an uncached load time under 20ms.

That was an extreme example of poor coding though. One final thought... if you don't go into the config and add the cache directories and cache everything, it will cause a slight performance hit on the server (though, probably not as severe as serving up a dozen extra files). I suggest enabling APC or memcache, or at least specifying the cache folder for it to store the files in.