Web mail can be done so many ways. There is no guarantee that your provider's sote will work 100% with the iPad. If available, you should probably see if you can use POP3 or IMAP to connect with the through he Mail app. Check their support pages for iPhone and/or other mobile device setup options.
Other than that:
Try tapping and holding on the link to see if a contextual menu shows up with Open In options.
You'll need an app compatible with the document type for this to work. If you want a general app that will organize and view (not edit) most file types, GoodReader is about the closest thing to file management app available for the iPad.
If Open in Safar is the only option, then do that. Once the document downloads into Safari, tap in the middle of the screen for Sharing and Open In options at the top right.