Stupid focus question of the day

I'm not a beginner, but I might as well be given this dumb question. But, I would appreciate an answer to what I think is a relatively dumb question. I'll try to be as succinct as possible.

Why is it that if I am attempting a photograph of a scene at a moderate to far distance that things can be out of focus?

I am currently shooting with a D80, and my question appears to be lens independent.

For example, yesterday I took some practice shots of my house as I'm going to be taking a team photo for one of my children. I set my camera up approximately 3 feet from the front of the house. I then took a series of pictures at various apertures to see which was the sharpest.

I realize each lens will be sharpest at certain apertures, but my question is why, in these photos, is the door so out of focus?

If I am using a zoom, and zoom in, focus, and then don't refocus then it will be better, but does it require this step at all?

Another example might be if I'm standing on one side of a lake and take a landscape shot with the other side of the lake 100+ yards away would the results be the same? I notice that if I zoom in and focus then things are fine, but if I don't then details in the distance are out of focus?

Thanks for your patience.