Speaking from experience here:

A. Larger agencies still do make commission on published fares. Also agencies like the one I work for, have net fares. Savings can be huge for the client.

B. More often than not, airlines are NOT allowing CC to be put on the ticket on CERTAIN fares. Meaning we must pay the CC fee(s)....

C. Of course I am biased here, but if they're a good TA, they are worth every penny (within reason). When things go south, we fight for our clients and our 25+ yrs of relationships with the airlines, often gets the client along ways.

Thanks