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I know Capital ships are normaly painted in chapter colors. But are fighters and bombers painted in the same way? I am bilding a full chapter. thats 1000 minis but I would like to do at least 1 of every ship type including fighters. I want to make sure I am lore correct As this will be a mian display set in my house.

When you say "chapter" you're referring to a Space Marine chapter, right?

None of the planes released for Aeronautica at the moment would be fielded by Space Marines as they are all Imperial Navy patterns.

Standard [non-Dark Angels, Space Wolves, or Deathwatch] Space Marine air power consists of the:

Thunderhawk

Stormeagle

Stormtalon

Stormhawk

Stormraven

Fire Raptor

Caestus Assault Ram

Overlord Dropship

These would be painted in their chapter colors and, if you want some inspiration, all of these ships have 28mm versions that you should be easily able to find.

Correct, I do mean the Marine chapters. I also understand they are flown by the imperial navy. But as an attachment on a battle barge would the fights be of that Imperial division or the chapter they are assigned to?

If I understand the question correctly, Thunderbolts, Marauders, Lightnings, Valkyries etc would likely remain in their respective Imperial Navy colors, as it would be very unusual (and possibly heretical) for a Space Marine Chapter to formally incorporate those units into their command structure. A Space Marine Captain or Chapter Master could emerge as the head of a military operation that includes fighter and bomber squadrons, giving him command over them (thereby allowing them to be temporarily attached to a Battle Barge, for example), but those Navy units would retain their own organization and chain of command.

With that said, there are campaign and army badges that are used by the Imperium to signify units common to a certain theater. This could be an opportunity for you if you're looking for visual consistency. For example, maybe a Thunderbolt is in its traditional Navy colors (camouflage, blue, grey, whatever) but carries a blue and gold stripe to identify that it's attached to an Ultramarines Strike Cruiser. This would allow for a bit of visual diversity within your display (given that the designs are very different from Space Marine blockiness, they'll stand out anyways, it may do well to emphasize that with color schemes), while still retaining a sense of cohesion through painting stripes on the wing, maybe the cockpit assembly, the tail, etc of the aircraft with those markings.