It's not that he doesn't trusted them to keep the existent of Lyoko a secret, it's just he doesn't exactly know them. He calls it an insurance policy, a sure-fire way to keep everything secure and later justifies it to himself because Sissi knew and she talked.
It takes time and effort but the spore, as he calls it, is created and during the next Xana attack he slides the spores into the weapon system and his acquaintances are infected. The existence of Lyoko cannot be talked about unless he allows it or circumstances prevent the secret from being maintained. The fact that they can tell the truth is important after all because if things get out of hand and the secret must be told, they need to able to speak it in order to save the world. As his acquaintances slowly become friends, he finds himself refusing to think about the spore because he knows if the truth ever came out than he friends would leave him for his betrayal.
And to the lonely boy who had no friends at all, he just can't have that and so the spore, the sign of his lack of trust, and greatest sin is forgotten and suppressed by his keen mind.
While Jeremy is content to force the spore out of his head, Xana is quick to detect the anomaly and plan on how to use to his advantage. However in time the program realizes that the spore must be continuously downloaded, as it were, from the same person to make it run faster. As such the decision to target Yumi is simply a logical deduction since Xana has gotten the farthest along with downloading the spore from her than it has had with Ulrich or Odd.
The usefulness of the spore in keeping Lyoko a secret is invaluable to the program and so during the one his attacks he ensures to infect both Aelita and Jeremy to further keep Lyoko and by extension itself a secret from the rest of mankind. In the meantime he begins to tweak the spore and program it for its own use.
After countless battles the program realizes that it needs a new warrior and William Dunbar is chosen by pure chance, the spore is injected during an attack and William begins to dream of what has been erased. As expected William confronts the others and joins them and then Xana strikes clear and precise and William Dunbar is enslaved.
The spore program has been so twisted that Jeremy doesn't realize the significance and if he recognizes any of his old code, the memories are suppressed too deep to make a difference, especially when he has no intention or desire to ever acknowledge his greatest sin.
When Xana is defeated, the blow back is strong enough to shatter the spores inside of Yumi, William, Aelita, and Jeremy due to Xana's code being encrypted inside of it. However Ulrich and Odd remain infected and Jeremy's treachery is only never discovered because neither of them talks about Lyoko to those who don't know about it.
Authors Note: Jeremy came off as a control freak here and there, Yumi being constantly targeted was never properly explained, and I'm convinced that William only remembered the Xana attacks because Xana had already decided to possess him.