I don't think hierarchies are necessarily bad, I just think that we tend to implement them in a crappy way where they become the playthings of people who are solely focused on gaming the system for their own benefit. Flat organization makes sense in small groups but that group still needs a leader who can act as the agent of the group when dealing with other groups. It's the representative democracy model which is needed when there are decisions that need to be made on scales larger than that of the group concerned. A leader can also and should act as a tie breaker and moderator when the group is divided or finds themselves unable to make a decision.

Problems arise when those leaders are unaccountable to the people that they represent, you need to have very strong customs and procedures in place that allow you to immediately recall the leader and replace them if they start acting in their own interest rather than the group's. This also requires the group to have good knowledge of what the leader is doing, transparency and a public record of the actions taken by the leader.