[Plugin: WordPress File Monitor Plus] htaccess file's been changed

It may be innocent, since actions such as changing your permalinks settings within WordPress would legitimately re-write your .htaccess file. I’d suggest inspecting your .htaccess and comparing it against a copy of .htaccess from a backup of your site dated prior to the report, so you can identify precisely what was altered. Once you know what’s been changed, you can tailor your response accordingly.

What andrewmills says.

The htaccess file can be touched by simply visiting the permalinks settings page.

If the MD5 hash hasnt changed then I wouldn’t worry about the warning.