Usually there are multiple ways to verify your site in Webmaster Tools, uploading the file to verify is just one of them. I seem to recall there's also an option to add a special
<meta> tag into your theme's header.
Something also to remember is that the URL to your site needs to be exactly the same as the one you submitted for Webmaster Tools (that includes having or not have www in it).
If you're still having problems, you'll likely get better help over on the Google help section as this question falls outside the realm of WordPress support. Best of luck!