How does zero gravity affect the human body when it come back down to earth?

Space ships are not made with artificial gravity.  Returning astronauts do have an acclimation period when they return.  This is similar to being on a boat for a few days and coming back to terra firma.

Also, humans can live fine in zero gravity as long as they have oxygen and nutrients.  All of our bodily functions are carried out using muscular contractions so fluids travel freely.  If anything, their back and joint pain is decreased because they don't have stress on weight bearing joints and they are allowed to heal.

Astronauts lose up to 25% of their muscle mass in as little as a week in space. As a result, often astronauts have to be helped out of their space craft, upon return to earth. This is a result of not getting the constant work out that we normally all get on earth from simple living in an environment that has constant gravitational force. A Russia cosmonaut was able to create a workout basically using bungee cords to fake gravitational force, but he had to spend two hours a day working out to simply reduce his muscle mass loss so that he can walk off the space craft upon return to earth on his own. This fact throws allot of doubt on those big head, pencil neck alien theories. If this sort of alien existed, after travelling in zero gravity and then landing on earth, they would break their necks.

Actually, that's one of the questions they hope to answer with the extended stay. So far, they know that it causes muscle atrophy. But since then, astronauts exercise on the ship to stay in shape. So I'm sure they will discover any problems and then find a way to fix them.

Also, I don't think they are phsycially bothered by the force (like your analogy with the fighter pilot). I think they are mostly just disoriented. Like if you get in a pool and do a few flips. You can't feel gravity pulling, so you don't know which way is up. It's the opposite with them. So they get vertigo. I actually can't rememeber how they combat that.

But I think that the space station itself rotates so that an "artificial gravity" is created.

Loss of muscle mass and bone mass, fluid redistribution from the lower body up, overall fluid loss, heart slows down, decreased production of red blood cells, balance disorders, weakening of the immune system, nausea and other less serious effects.