For raw freighting the Atlas i indeed better in every situations. But it still cost 24.000, which is a lot early game. Also, in a bad engagement when you must retreat, your Atlas don't stand a chance and its loss is a huge toll for your fleet.
Early game, the Tarsus is interesting because of its tankiness and burn drive. You can still deploy it as a point defense platform or meat shield during a battle. If things get ugly, the burn drive ensure it will get away fast.
The Mule is also a very good choice, it's a combat freighter after all! It can provide quite a lot of firepower and tankiness for an early game fleet. If you need a carrier and a long range fire support, the Gemini is the obvious choice.
For an optimal end game fleet though, then yes, Atlases with tugs is the most reasonable. Or Hermes and Hounds for a frigate based fleet, at end game you'll never deploy your freighters anyway, even the armored ones. That's when your chart shine.