In my current game, the pesky civilians have 3 freighters on the Earth - Mars run moving infrastructure and I have 4 on the Mars - Titan run taking the "free" infrastructure.
I am not sure what to do about the free infrastructure once I revamp the raison d'etre of civilian shipping (which I am in the midst of at the moment). I might make infrastructure either cheaper or easier to transport, probably the latter given the larger freighter sizes and the fact that transport requirements rather than cost seems to be the main restriction on infrastructure.
Given my 4.0 experience so far, I would vote that the free infrastructure from civie freighters remain free, i.e. have it fall into the same bucket as "no maintainence requirements for civilian shipping". The reason is "yet another thing that I don't have to micromanage in a colony". At present I've got two populated worlds: Mars (pop 30M, cost 2.8 ), which the civies have pretty much completely colonized on their own, and Epsilon Eridani (cost 2.2), which is two jumps away. The fundamental difference between them is that the civies can't get to EE, since I haven't researched jump gates yet. At present, I'm leaving Mars on (civie) autopilot, and colonizing EE by hand. The game-play tradeoff that I'm battling is when to research jump gates and build them - once I do, I can move the autopilot to EE; until I do I have to use military resources (including building and shipping infrastructure) to grow the EE colony. pre-4.0, I would have had to bind a freighter to the Mars-Earth run carying pure infrastructure, then make sure that whenever I was running low on infrastructure that I scheduled some infrastructure construction in the queue. I would have to do this check by hand, since there's no way to be notified when the infrastructure pool on Earth is running low, or to schedule some % of industry capacity to infrastructure production. This resulted in a LOT of micromanagement of the production queue. Now, I don't have to screw around with that, and can concentrate on trading off between building e.g. fuel factories or research labs.
To summarize, I think the current state of infrastructure (civies get/place it for free, but military has to build) is "just right" - it allows players to set up the environment (by declaring colonies and building jump gates to them) and strategic goals (by declaring whether colonies are sources or sinks) for civies to do the colonization, while still putting a cost on non-civie colonization.
John