Open a terminal window, and type "file ~/Downloads/.QT" and hit the tab key - it should auto-complete the name for you. If not, type it out manually. Then hit enter, and if it can, the utility will tell you what kind of file it is. You can then open it in the appropriate application and see what's in it.
No matter what it is, it's likely to be safe to remove, unless you have some weird application that stores critical content in hidden files in your Downloads directory.