As an alternative to write-protecting the file, you can open %userprofile%\Documents\My Games\Fallout4\Fallout4Prefs.ini, and in the [Launcher] section, add bEnableFileSelection=1. This doesn't actually enable mod selection in the launcher like it sounds like it would, but it does stop the launcher from undoing changes to plugins.txt. I think this is a better idea than making plugins.txt read-only, because I'm afraid what will happen once mod managers start coming out is that people will forget their plugins.txt is read-only and be wondering why they can't change their load order (although maybe the mod managers will be smart enough to make the file writable before they try to change things).