I've been finding that with a colony, I park what I don't need. If I'm doing exploration, I can get away with a small, cheap fleet. If I'm doing bounty missions or need to defend the colony from a raid, I pull out the expensive heavy hitters. That mitigates a lot of my running costs I find.
I've been playing a lot of spacer/iron man and after a number of runs I think I'm getting a feel for how to do that start successfully. Although Iron man does tend to mean I restart quite often.
Spacer introduces the complication that your levels actually have an in game credit cost (i.e. 1,000 credits per level per month), which means initially you want to stay low level while building up an initial bank account. I will point out this is somewhat unintuitive game play (generally one might assume being higher level is better) and I'm not sure if this the gameplay Alex was going for with the spacer start, although given he's hidden it in a settings file I'm guessing he also doesn't think its ready for prime time.
Even exploring will provide XP, just not nearly as much as combat, and so for skills, I grab Navigation 3, and then Fleet logistics 2, in that order. The strategic options provided by Navigation 3 on an Iron man run are invaluable (both in terms of keeping at 20 speed sustained burn and simply escaping a system at any point).
Anyways I tend to accept a bunch of exploration missions over 15-30 days while hanging around the core sector doing a delivery mission or two, or perhaps some drug or weapons smuggling, and then do a grand tour of the sector to complete the exploration missions. I can generally do 3-6 exploration missions in ~120 days (150k-300k) plus a delivery for another 10-20k. This tends to be low experience gain, especially if you just run the sensor package and don't actually salvage the target (or especially fight the defenses).
This typically will let me build up credits at a steady rate over time with a fairly small fleet. Each cycle is basically enough credits to buy a cruiser. Given I'm not fighting, the playtime goes relatively quickly, although still quite exciting when you realize you accepted a mission for a yellow or red warning system. To be honest, I find myself actually using the stealth mechanics and have started seriously considering grabbing the sensors skill.
My objective during this time is to get enough credits to start a colony, build a profitable industry, get a starbase, and enough destroyer and cruiser class firepower to handle the first pirate fleet that comes for the colony and enough firepower to take out a tier 1 pirate base. At that point you can start to relax, as your trickle of income is enough to at least offset the crew costs plus monthly debt. When I do explore missions after that, I'll leave the combat ships at home and still use my low cost exploration fleet, which minimizes my running costs.
Depending on what ships you happen to come across exploring/salvaging, you can get started on 0.5 to 1.0 million credits I think. 500,000 towards the colony and first few buildings, and 500,000 towards a cheaply bought destroyer/cruiser fleet (500,000 should be enough for 3 cruisers). If you found some salvageable cruisers (or capitals) during your exploration phase, you can probably get away with less.