A few other issues:
They, as far as I can tell, don't have access to any better discounts that you could find on your own.
You lose all control of your reservation, so any changes up to maybe 3 or 4 days before your trip can only be handled by them. If you have a flaky TA it could be very stressful making sure everything is setup right.
Since they no longer get much if any commission on air fare, you have to handle that part of your trip.