The flail became a very popular weapon due to its small size, low cost, and ability to deal a fatal blow in one hit.
With every form of armor, there were trade-offs. While plate-mail could deflect just about any form of weapon available, it was heavy, expensive, and it greatly reduced movement. Chain-mail became popular because it was light-weight, very strong for its size, and would turn away bladed weapons (but not arrows).
The flail, however, was able to maim and kill the person under whichever form of armor he chose to wear. A simple one-handed flail with a two-pound weight on the end, when wielded properly, could produce a blow with 800 psi of force. This was more than enough to crush skulls, helmets, and skulls under helmets. Chain-mail was especially weak against the flail, as this armor was designed to be flimsy and light-weight. Even the sturdiest iron helmet could be crushed by a single blow from a flail.