It depends on context. It can mean “That [what you said] is exactly right.” It can mean “That is the perfect thing for the situation.” It can mean “You have identified exactly what the problem is.”

It can also not really mean anything, and can be used as you go to further some point in a conversation. "He's a moron." "That's just it though, he doesn't seem to be a moron until you get to know him a bit better.

Hi this is EJ Jarabe from Philipiines. That's just it means That is exactly the problem or the issue.