How can I get Dreamweaver to read the .htaccess file so that it can find all the related files properly?
Dreamweaver CS5 will use your .htaccess file in Live View, but that's no use to you in discovering related files for editing. However, you can set up Site-Specific Code Hints in DW CS5, which provides code introspection and code hints for files that are not necessarily directly linked to the current page. Also DW CS5 will discover dynamically related files.
None of this works in versions earlier than CS5.