I apologise. This is a rather Wikipedia esk put-together little piece, but I would like to correct and explain a misconception that iss till going around.
Karate and Kobudo were not trained in secret at any point in its history, nor was it ever banned. Because the people who did it were part of the samurai and upper classes who were allowed to do it. For your peasents, yes. The Ryukyu king Sho Shin had banned weapons in 1477, and the Japanese Satsuma clan continued this in 1609 and a more extensive ban 1669. But then why wasn't it driven underground if it was banned?
Because the people we get our karate styles from Okinawa, the first generation of masters if you will, were the nobility. They were the ones allowed to keep training it, because as samurai that was their whole job, to be proficient fighters, and as the years went on and the class expanded as their class heritage.
The most obvious example of this is Motobu Choki, who was just straight-up nobility. There were several exclusive styles for the main royal family.
Funakoshi was a member of the Shizoku, a class formed after 1869 when the Meji restoration abolished the feudal system and would be more like a petty nobility in a western sense, in that they have a class but nothing much more, it doesn't given them any inherent wealth or power like the higher classes, but he was still part of it. Most of the others, like Chōjun Miyagi and Kenwa Mubuni.
Anko Itosu, going back a generation before the Meji changes that gave an amalgamated Shizoku class, was part of the Yukatchu. Part of their role was military training and preparation, including hand to hand combat. It was literally their job to do it, and this goes all the way back to King Sho Shin. Soken Matsumura, another of the legendary predecessors to the style founders, was Chikuden Pechin, another member of the Yukatchu, and was employed to teach the royal family martial arts.
Karate comes from the hand to hand combat arts of the Ryukyu samurai and nobility classes. It was not hidden. There was no hiding or improvising weapons or movements as something else to hide from the authorities. The people we trace karate back to were the authorities, there was a ban on martial arts, but they didn't apply to these people. This is not an art from the peasents or farmers.