Please note that this holiday is no longer officially known as Boys Day in Japan. It is now called kodomo no hi which means Children's Day. In the past, the significance of the day was that it was a day for doing various things to help ensure that the sons of a family would grow up to be strong and manly. The most visible of these things was to fly the koi nobori carp flags. These flags (when blown by the wind) resembled carp swimming upstream. Carp are said to be very vigorous in swimming upstream against any difficulties and Japanese hoped that their sons would have this same trait.
Nowadays, with Japan trying to be more inclusive, the holiday celebrates all children. It is simply a day for celebrating children and expressing the hope that children will prosper as they grow up.