yep, i am one of those people that used militaryfares.com and showed up at the airport and was told i didnt have a reservation. I purchased a ticket traveling from seoul, korea to orlando, fl and the money was taken out of my debit card. When i tried to check in, i was told i didnt have a reservation, I even printed out the email page with my booking number but as the first post mentioned, its only a booking number, not a confirmation number, so it was essentially worthless. It was suppose to be an 8am flight, and since militaryfares.com do not have a phone number listed on their website, my only option was to call the airline office, which opens at 9am. since that would be too late, and I had to travel that day, i purchased a ticket on expedia to fly later that afternoon that cost more than twice the original amount. I opened up an inquiry through their website and received a response later that day claiming that they had sent me an email stating since they couldnt confirm one of the segments of my flight, the whole reservation was cancelled. I doubled checked all my emails, because i didnt delete any of them, and of course, no such email. I ended up getting refunded the original plane ticket, but still i had to pay basically double for the other ticket. I have held a company commander position and have advised everyone i have been in contact with to NEVER, EVER use this website

The to OP. How can you say you disputed it with the credit card company and they told you to deal with the company first - unless you tried to cancel your ticket reservation and get your money back BEFORE you flew. If you tried to cancel the charges before the flight (FYI, you probably purchased a non-refundable ticket) than no credit card company is going to do that. You bought the tickets, etc. So how did your flight turn out? Did you get any charges afterwards that were extra that you referred to?
I've disputed credit card charges a couple of times in my life and was never told that I had to deal directly with the company. You follow your credit card companies instructions on submitting a dispute with them. The credit card company then does all of the leg work in verifying the dispute - not you! If the credit card company cannot get information from the company or they determine outright fraud...they will eat the charge. There is something fishy about your story because if you had a filed a dispute than it would have been handled that way. I think you tried to cancel your non-refundable ticket "BEFORE" flying and your credit card company said no, at that point, you would need to deal with the merchant...which makes perfect sense. Please clarify - I noticed you posted about them on Military.com with the same paragraph.
As to MilitaryFares.com - if that is one of your representatives who wrote that response...you need to either fire them or ask someone with proper English skills to write your response! I have bad English myself but your post seemed like it was written by one of those Nigerian E-mail scams from General Edajladai and his Millions that he wants to share with me!