Travel agencies (including online ones) tend to use the airline's merchant account when issuing tickets if it is published fare that is found in the GDS. Your credit card bill will show up as "Singapore Airlines" (provided the travel agency inputs your credit card number into the "form of payment" field of your PNR and use the GDS [as opposed to their own credit card machine] to obtain credit card approval). As far as the credit company is concerned, you would be spending directly with the airline.

Only when certain discounted/bulk fares are issued (or when the "form of payment" is entered as "cash", "invoice", "agt", "check" etc.), would the travel agency's name show up on the credit card bill.