Is ergodic hypothesis in contradiction with the notion of equilibrium?

You have to be careful to distinguish between microstates and macrostates. Thermodynamic equilibrium is a macrostate which consists of a mixture of all possible microstates of energy $E$ weighted by a Boltzmann weight $e^{- \beta E} / Z$. A state in macroscopic thermal equilibrium can be thought of as "moving through phase space" ergodically (i.e. the microstate is constantly changing, but the fraction of time spent in each microstate is fixed to the Boltzmann weight).