tap water got very rusty

I have a 500 foot well. It is about 10 years old. The house and pipes are about 45 to 50 years old. The water has had a little rust in it (settlels to botom) but suddenly it started to come out almost orange/brown in color. What does this mean? I have a water softner hooked up to all pipes except the cold water in the kitchen. The kitchen cold water is the only one effected.

What kinda plumbing system? We had same problem growing up as a kid Galvanize steel plumbing.

Yes this could be caused by galvanized pipe somewhere in that cold water line but... it also could indicate an iron problem in the water from the well. This demonstrates why it is best to 'soften' all the water in the house instead of running hard, iron water to the kitchen sink cold.

It' better

Our house is on a slab and the way that the pipes are hooked up there is no way to hook up the kitchen cold water. The problem seemed to almost go away later the same day. I was wondering if it could have anything to do with a very large amount of rain?

I believe there's a number of iron loving bacteria that can also cause the discoloration you're describing. I'm not sure what the recommended treatment is or how to test for them (though I'm sure someone here does) but if you search online you'll find lots of information such as here:
http://www.agric.nsw.gov.au/reader/financial-recovery/ac2-solubleiron.htm
Good luck.

Yes it could have to do with a large volume of rain raising the water level in the well.

It could be a slug of IRB (iron reducing bacteria) breaking loose. But if the water is/has been odor free, that is a remote possibility.

Do you have any type of water filter or softener? If so, by-pass them one at a time and see if there is any improvement. If so leave the one by-passed that causes the discolored water and call a water treatment dealer for service. If no treatment equipment, get a water test done and buy an appropriate filter etc..