You say Frontpage doesn't like it.
FrontPage doesn't like it in some cases and doesn't care in other cases. The solution is to make a backup copy of the original .htaccess file and make whatever changes you want. If the extensions stop working, simply replace the original .htaccess file.
What if you used another editor, would the problems stop
Yes, the conflict is between the FrontPage extensions version of the .htaccess file and whatever changes are made to it.
Another choice is to continue using FrontPage but not use the FrontPage extensions. Using FrontPage without the server extensions eliminates the problem. Just don't use any of the features in FrontPage that require the extensions.
List of components in FrontPage 2002 that require FrontPage 2002 Server Extensions:
http://support.microsoft.com/kb/281532/en-usYou can tell FrontPage you aren't using the extensions by selecting the Tools menu and choosing Page Options... Authoring tab... and for "FrontPage and Sharepoint Technologies" select "None".
If you choose to not use the extensions, you will use the FrontPage FTP publishing option to upload your web changes.
If you inform FrontPage you are not using the extensions, then menu entries will be disabled for features that require the extensions.