Sometimes you can't use your Dexterity bonus (if you have one). If you can't react to a blow, you can't use your Dexterity bonus to AC. If you don't have a Dexterity bonus, your AC does not change.
Flat Footed means losing your Dex Bonus. It says nothing about a Dex penalty.
That's my assumption as well; is there a page reference or anything which states the rule? Trying to clear this up for a druid wildshape spreadsheet being put together for the community.
Edit: Didn't see Doomed's post until after I posted. That settles it, then. Thanks!