Create user.js file for Thunderbird with the preferences in it.
Thunderbird Help: Editing Configuration Files
http://www.mozilla.org/support/thunderbird/edit
user_pref("network.protocol-handler.app.ftp", "/usr/bin/firefox");
user_pref("network.protocol-handler.app.http", "/usr/bin/firefox");
user_pref("network.protocol-handler.app.https", "/usr/bin/firefox");