It's not as if they were using it as a freighter. Most of the time, when the ship was mentioned as transporting cargo, it was cargo of humanitarian or diplomatic importance.
Also if the Enterprise had just completed a mission near Point A and was travelling to its next mission near Point B, the Federation might send whatever cargo was going from A to B on Enterprise since it was going that way anyway. Why waste a freighter's time when a starship is already going there.
It seems that most of the mentions of cargo ferrying by the flagship were out of necessity: the cargo was vitally important (i.e. medical supplies to stop a plague or VIP personnel) or they were the only ship nearby who could move it in the time limit. I don't recall ever hearing about self-sealing stembolts being carried, if that's what you're implying.
Real World Example for the above, many countries use Military assets to transport cargo when it's needed for humanitarian reasons.
So to sum up:
1) If the delivery of the cargo was time sensitive (like delivery of needed medicine), then you want a fast ship to deliver it (few ships were as fast as the Enterprise).
2) If the cargo was politically important (like Kamala), then you want a ship to show it's political importance (few ships had the political importance of the Enterprise).
3) If the cargo was highly valuable to the Federation, then you want a powerful ship protecting it (few pirates or raiders would choose to challenge the Enterprise).
4) It could be a matter of convenience (we have cargo that needs to go from Planet-X to Planet-Y, and hey, the Enterprise is passing the general direction of both Planet-X and Planet-Y; they can carry the cargo).
5) Since Starfleet is a research/exploratory organization, not a military organization, transporting cargo in support of research operations at one Federation site to another.
Another possiblilty to consider is that maybe some of the cargo we see onboard is consumables (spare parts, replicator matter, emergency supplies, fuel) for the ship or crew to use, they've got to store them somewhere, and the Enterprise is designed to be able to operate away from a starbase for extended periods.Cpthunt 07:23, September 7, 2011 (UTC)