Are you sure? My ships are definately not being resupplied just being in system. I think you must still go to a planet with a resupply depot. Unless you have some advanced tech which can accomplish this....
Like Kwok says. It really confused me the first game too; I was sure it was 500( 1000 with Balance mod) for each ship each turn, so I thought I wasn't getting supplies at all. Turned out I actually was getting supplies, but spread out on all my ships it was hardly noticable.