I'm applying a widescreen filter to a shot I had to slightly straighten out... but the widescreen filter tilts along with it.

Any idea how I can straighten my image without the widescreen filter tilting as well?

Yeah, I know... 'rookie.' :)

By "straighten out" I assume you are talking about the stabilizer stolen from Shake.

This indeed has the unattractive effect of zooming and skewing the footage.

It's color solid in FCP. The default is blue, so you'll have to change to black. Make two layers above your video track. One for top and one for bottom of the letterbox. Use standard alignment from real letterbox or program letterbox.
Adjust as need.

Hope this helps.
-C

Here is a screen shot.

Thanks Christopher!