Flaws are ok, as long as they don't make them unsympathetic.
I don't have to feel sympathy for a character to really find them interesting and enjoy watching them. I never felt much empathy for Dukat and he's one of my favourite Trek characters before S7 butchers him.
For protagonists, like Sisko, you should be able to empathize with them. They are, after all, our proxy in the world.
The problem I have is that the main character trait that characters express the most in DS9 (Sisko excepted I guess) is selfishness. Now that's easy to identify with, as most people are selfish almost by default, but I don't find it an appealing trait in a protagonist, which is why I also don't like the JJ Trek characterizations, where Kirk is highly self-centered.