Completely agree. To prevent you from bringing CPAP on board is a violation of federal aviation regulations. See 14 CFR Section 382.41:
(b) Carriers shall permit qualified individuals
with a disability using personal
ventilators/respirators to bring
their equipment, including non-spillable
batteries that meet the requirements
of 49 CFR 173.159(d) and any applicable
FAA safety regulations, on
board the aircraft and use it.
(d) Carriers shall not, in implementing
their carry-on baggage policies,
count toward a limit on carry-on
items any assistive device brought into
the cabin by a qualified individual with
a disability.
See also
http://airconsumer.ost.dot.gov/rules/20011029.htm
"The limit of one carry-on bag and one personal bag (e.g., purse or briefcase) for each traveler does not apply to medical supplies and/or assistive devices (including service animals and their equipment). Passengers with disabilities generally may carry medical equipment, medications, and assistive devices on board the aircraft."
I occasionally get looks from my fellow passengers about the third bag, but I have never ever had a problem from TSA or the airlines. (Although I once had a rent-a-cop ID checker at BOS give me a hard time, but as soon as I pushed back, she let me go).
I agree you need to file a complaint.