Flood damage is the first thing I'd suspect when there's rust in
places where there usually isn't ...you should look for rust in other
normally non-rusting areas like the metal dash parts and seat
mechanisms.

(More things to look for:
http://www.betterbusinessbureau.net/disaster/auto.asp)

If it just looks like surface rust, there's not much cause for concern
structurally (it could have been a bad day for the robot that coated
it at the factory).
However,  if there is rust in other places, there could be some
corrosion in the electricals...which is cause for concern.

Since this is a convertible, it could have been caught in the rain
with the top down and wasn't dried out properly when it was closed (or
the top leaks).

My '97 convertible has some rust specks on the pedal levers, but it
looks harmless...and the car spent the first few years of it's life
near salt water.

Try going back to the dealer and requesting a Carfax report
(especially if you find more rust)...I suspect if a flood/water damage
claim was made, it would show up.
http://www.carfax.com/

It's a ragtop, coulda rained at one point in it's career while the top
was down. As long as there is no serious rust anywhere else on the car
I wouldn't get excited. Seems there should be at least a coat of paint
on the pedals to prevent such a situation. Is it rusted thru the paint
or are they bare metal??