Each house that has a military has lawful trader factions. These factions fund their new members to give them new ships, etc, usually by getting a fee from their members. 10% on each trade run or some such is usually enough to fund them.
Now, someone mentioned the governments being the ones to pay the military. So they can be.
How do governments gain money? Taxation.
Who has the money? Trading corporations.
Who benefits from extra police/military? Trading corporations.
'Do the math', and we get:
Trading corporations donating a set percentage of profits to the military high commands to dish out as they see fit.
The "Big three" Liberty corporations as well as any smaller ones can contribute to Liberty's defences.
The Rheinland corporations (ALG, Republican, etc) can contribute to Rheinland's defences.
And so on.
Naturally, there won't be as much money as you can make by trading, since that's obviously not what any of us want. Just enough cash for upkeep; b/bs, ammunition, and a bonus or two for the dedicated cops or kills scored if they see fit.
The only people set to miss out are the Indies. The Independents should be encouraged to join factions, since it improves role-play experience for everyone. What better way to bring people into the fold than to offer them a wage for what they're already doing.
I don't propose to speculate on what the wages would be, whether higher ranks would get more, or anything of that nature. That would be for people in charge of the respective military faction to decide, based on how much money they're getting from the corporations.
Point is, if it's only a percentage of the trading faction's profits, it won't be more than the traders themselves are earning.
No need for admin magic making the money appear, no need for people to feel trading is obsolete (how else're you gonna get that shiny cap you want?).