Got my answer.... (bolding added for emphasis)
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Dear Mr. Rebel,

Thank you for contacting AirTran Airways.

Please be advised, all fares and schedules are subject to change without notice. Our special fares are available for a limited number of seats and are very popular with our customers. However, should you find a fare offered at www.airtran.com which is lower than the fare you originally purchased directly from our web page, AirTran Airways will honor a fare adjustment in the form of a reservations credit.

Unfortunately, AirTran Airways does not match fares offered by other airlines or by other travel websites. I apologize for any disappointment this may bring. However, our records do indicate your reservations were booked via Kayak.com, not directly at www.airtran.com. Nevertheless, your comments have been forwarded for further review and future considerations.

If I have failed to address all of your concerns, please let me know in a reply to this message. Your continued support is important to us. We thank you for including AirTran Airways in your travel plans and we wish you a very pleasant flight.

Sincerely,

Jodi XXXXXXX
Customer Relations
AirTran Airways
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That just stinks... I think it is sneaky to say that since I came to airtan.com via a link on Kayak that they will treat me differently than if I went to airtran.com directly.

Since the free seat selection is gone from Kayak, and now this. I will NEVER click through from Kayak again. I'll still search fares there, but that is it.. Hrrmmmppppf!