There's nothing wrong with TWF and Flurry of Blows. When the monk is using weapons, it merely means something different. Most Monks I've seen don't use weapons, though, just their fists. In these situations, TWF and Flurry of Blows work just fine.
Also, if you're TWF with a weapon and you get a flurry-like ability (like with the Exotic Weapon Master), the two also work together.