I mean, it depends on what you're doing, and what skills you have, and what sort of fleet you're lugging around; I
generally don't have issues with supplies these days, but I'm also decently skilled at the game and can, for example, generally expect to come out of a battle with more supplies than I went into it with.
Particularly early game, it can be enormously helpful to go three or four skills deep into Industry, even if the intent is to respec out of that later.
Late-game, the benefit of a good colony setup is disposable income - when you're making hundreds of thousands of credits a month just for existing, you can afford to buy supplies wherever.
Pirate bases can also be excellent sources of supplies - they've got relatively low defenses against raids, so just one or two hundred marines can easily top off your reserves.
Also:
I am currently using a mod that gives you income for signing up with a faction so that helps with the cost a bit but if I wanted to play independent I'm not sure how you would support yourself.
This is a vanilla feature. Holding a commission is highly profitable; the tradeoff is that you always have enemies - and frequently have unexpected enemies, too.
I am finding it difficult to keep supplied with a larger fleet without bankrupting myself.
What, exactly, do you consider to be a 'larger fleet'? If you're lugging around a half-dozen Onslaughts and Legions - yeah, that's a really very expensive fleet to run.