Why are all the auto/scene modes apertures set to 3.5?

I use a nikon d3000
and i was wondering why i can't change the aperture out side the A mode.
and why it it set to the smalled F-STOP.

On what lens? 18-55mm?

That's because if your camera senses it being anywhere close to low-light, then it will automatically stop down.

Actually, the only situations to were it would change to a higher f-stop, is in bright sunlight.

You shooting using auto modes in low light. Smallest aperture lets in the most light.

Learn manual exposure and better still off camera flash if you want to be the master not the slave.

Well obviously you know aperture controls how much light hits the sensor.
First to be clear, you doknow that the relationship between aperture and f-number isan inverse one, right? As in the number 3.5 indicates a larger aperture (so more light hitting sensor) than say the number 5.6.So assuming you want to keep your shutter speed at 1/60 and your ISO at 400, in very bright light you'll need to set your aperture very small (say f22), with slightly more reasonable light levels you'll need a larger aperture (say f8), in dim light you'll need a very large aperture (say f3.5 or f2.8 or maybe even larger).

Anyway;

In full auto the camera is likely to try and choose a shutterspeed fast enough to hand-hold (in low light that means as large an aperture as possible, assuming you're using the 18-55 lens that's f3.5)

When youhave the camera set to shutter priority, you may actually be able to get it to change the aperture, try setting a shutterspeed of say 30 seconds and unless it's really dark, you'll see the camera choose a smaller aperture.

To put it simply the camera is choosing f3.5 to get as much light as possible into the camera and consequently keep the shutter speed reasonably high.