On a side note the DOT has been pretty aggressive assigning penalties (around $40,000 - 80,000) for violations of the full-fare price rule (part of 14 CFR 399.84) that went in to effect on 24 Jan 2012.
If you feel that you were over charged on bag fees then apply for a refund with the airline (note this type of refund generally cannot be done at an airport ticket counter or ticket office) citing 14 CFR 399.87. If your refund is not approved but you feel it falls within the requirements of 399.87 file a complaint with the US DOT.
http://airconsumer.ost.dot.gov/CP_AirlineService.htm - Airline Service Complaints and Comments
Complaints may be submitted online at the above web site, by phone 24 hours a day at 202-366-2220 (TTY 202-366-0511) or by mail at the address listed on the above web site.