1999 HONDA CRX User Comment / Complaint

On 1 feb 05, i took my 99 honda accord, vin # 1hgcg1645xa011445, to a honda dealer here in fort walton beach florida due to sluggish acceleration. they told me that the transmission system needs to be replaced for approximately $3,700. i asked them why the transmission would breakdown at 47,000 miles only. they said it is no longer covered by warranty but they will check with honda hqs. later on the day, they called and said honda will pay for the parts but i have to pay the labor cost ($504) to replace the transmission. my question is: why do i have pay for the labor if they agree to provide the parts. i read that there is a lot of problem on honda transmission so i presumed it is a factory defect. is there anyway you can help?