I'd say that the Apogee is the best choice. You have firepower, speed and carrying capacity. The problem is they are hard to find and are very expensive.
It really depends on what you want to do. The Apogee is a burn-3 cruiser, which means that using one as your cargo-hauling solution limits your speed to whatever you're willing to make a burn-3 cruiser do when part of the reason you chose that particular cruiser is its cargo capacity, which means that any fleet which would otherwise have consisted of fighters, destroyers, frigates, or burn-4 cruisers will be slowed (assuming none of the ships are D variants with Degraded Engines). They also carry significantly less cargo per per point of logistics than dedicated freighters like the Buffalo or primarily-freighter compromises like the Mule, though in terms of cargo unit-lightyears per unit of fuel the Apogee is on par with the destroyer-scale dedicated freighters and superior to the frigate-scale freighters (the Venture is slightly superior to the destroyer-scale freighters by this metric).
There is also the question of risk. An Apogee may be a good compromise between pure-warship and pure-freighter, but using it as a warship puts your cargo capacity at risk, while leaving it in the reserves is inefficient by comparison with a group of dedicated freighters with equivalent logistical cost or cargo capacity.
For the logistical cost of an Apogee, a small trading fleet could have 5 Buffaloes for 1500 cargo and probably won't miss the Apogee's firepower unless that was going to be the only escort; other groupings with similar logistical costs are an Eagle and a Buffalo, 550 cargo to the Apogee's 450 and with roughly comparable firepower, or a Falcon and a pair of Buffaloes for 750 cargo and +1 burn speed unless you have something with Degraded Engines or already have a capital ship or burn-3 cruiser in the fleet (granted, Falcons are much weaker warships than Apogees, but that shouldn't really matter to a trade fleet). A small bounty or pirate fleet is more likely to take the compromised cargo capacity in exchange for the increased firepower offered by the Apogee, though larger fleets have enough room that you could easily decide to have a small group of dedicated freighters supporting heavy warships or carriers and come out roughly even with the Apogee route (e.g. Eagle + Buffalo, ~11.6 logistics for 550 cargo versus the Apogee's ~11.5 logistics for 450 cargo, or 2 Dominators + 1 Buffalo, ~22.1 logistics for 800 cargo versus 2 Apogees for ~23 logistics and 900 cargo; the latter alternative offers considerably greater firepower for very little loss in cargo capacity, while the former offers roughly comparable firepower with somewhat superior cargo capacity, though the former option's staying power might be a bit lacking).
Which choice is best depends on what you want to do and what compromises you're willing to make. If you want to run a small bounty hunting (or pirate) fleet where most or all of your ships are likely to see action in any significant engagement, then sure, I could see Apogees being one of the more suitable options. If you want to run a trading fleet where avoiding combat is your preferred route, then I would tend to think cargo capacity and speed would outweigh firepower, and there are lots of options for getting an escort heavy enough to deal with the pirates who can catch you and fast enough to avoid tangling with the pirates who can take you while keeping a higher cargo capacity and burn level than the Apogee would allow. If you want to run a big combat-oriented fleet, there are plenty of ways to stack freighters with combat ships so that you're getting about the same or better overall fleet cargo and firepower than just going with Apogees would, and sufficiently large fleets are large enough to not worry about having a few noncombat ships in the lineup; after all, they have plenty of other ships to do the fighting.