I do not use Atlas anymore unless I need to haul a bunch of commodities from one colony to another (to prepare for shortage mitigation). Colossus or mass Apogees seem to do the trick for general loot hauling. Even Colossus 3 is nice as a dual-purpose ground raider and hauler.
Prometheus is useful if I need to haul a lot of fuel (since there is no cruiser tanker), and can squeeze Augmented Engines and Efficiency Overhaul.
The big spike from cruiser to capital is the main reason I avoid too many capitals in my fleet, especially haulers that cannot fight. Once, I scuttled my Prometheus because I needed to cut fuel use (due to too low fuel), and it was the cheapest and most expendable ship to replace.
EDIT: If bar mission rewards scale based on how much cargo space I have available, then bringing several Atlases could be handy for triggering those fat reward missions instead of usually seeing those that only offer pocket change.