Does this happen with any pdf anywhere, or just at a particular site?
Just asking because some websites employ lame* plugin checking. If they do not find the plugin they do not even try to send the pdf to your browser.
(*I say lame because some code used for this does not always work with all browsers, especially with built-in pdf viewers.)
If you have not already done so, try checking a pdf at another site.
You can also check Safari's pdf abilities by using a pdf file you have on your computer, either drag it onto an open Safari window or use File > Open from within Safari.