There are some things that he won’t confide in to anyone. Ever. He would spill embarrassing moments from his youth, discuss why his marriage fell apart, even talk about his feelings before he would talk about his dreams. They were something personal that kept him anchored when his mind was trying to fly into the sun.
Because really: Stargates? Aliens? It was the stuff from every trashy tabloid that he‘d never admit to reading. That was before he even took the plunge and discovered a submerged city, vampire catfish, and Amish who didn't turn the other cheek.
To think, those were just the highlights of his new life. And really, once he got used to how things worked in another galaxy, it wasn’t too bad. Weird, but surprisingly fulfilling. When he put together a team together at Elizabeth’s behest, he felt like he was finally home again. Most missions that they went on were fraught with danger, but it was their trust and compatibility that pulled them through. He trusted each of them with his life every day. It still didn’t mean he would tell them about the things he's seen and heard, long after the expedition is asleep, with only the skeleton crew keeping things running smoothly.
At night he dreams.
He doesn't tell anyone about how the first time he realized that something was weird at the Antarctic outpost -- because with all the top secret projects the government was allegedly working on, a glowing yellow squid thing attacking you was pretty minor on the weird shit scales -- was when he heard the ancient (not yet Ancient) chair whisper to him. It wasn't a language he understood; it wasn't calling “Johnnn, Johnnnn!” It was just projecting interest, and comfort; trying to get him to sit in it, to give it life again.
Maybe this subliminal calling was what scared Beckett so much about it. His gene was very weak; it was possible that he couldn't really hear the chair, just a strange undercurrent of unease.
It seemed to be gently inviting John to sit down, and it didn’t seem to be dangerous. After all, what harm ever came from sitting in a chair?
Boy was he wrong! No harm came from sitting in the chair (not directly at least), but it did open a whole new world for him, and the people chosen for the expedition, leading John right to his next problem.
City of myths and legend, with a history longer than any civilization's on Earth. It was eager to show John what had happened within it‘s halls. Every night he spent in the city, lulled to sleep by the ocean, he dreamed. Atlantis showed him scenes; snatches of lives lived within her walls; snippets of music and laughter; bright births and solemn deaths. And later, she showed him their fear, and grief, the horrible realization that the only hope was to abandon their beloved City. He feels so much a part of Her now that he thinks if he ever had to leave he would know exactly how the Ancients felt when they left.
McKay already calls him Atlantis' Golden Child, with capital letters and all. Telling him about these dreams would only fuel his teasing, and his not so subtle envy. Telling Elizabeth was out of the question. She would want him to tell her all about them, describe them to her, when they are supposed to be for John alone. His connection to this galaxy. Let Rodney have his science, Elizabeth her hopes and dreams. John just wants the City.
Some days he thinks he should visit Dr. Heightmeyer. But he knows he's not crazy. Maybe slightly unbalanced, because he did come to a galaxy far, far, away after all. Overall, he's not crazy though, and he doesn't want to share his link with the City.
So, he never gets around to telling anyone how much he's connected with the city. It may not be the sanest course of action, but it brings him the most comfort.