Were the Waldensians like a Protestant Church in the Middle Ages? I do not know anything about the Waldensians. Specifically, do we actually know what their doctrine was and why the Catholic Church opposed them?
Most information about the doctrine of first valdensians that survived till today is contained in the inquisition protocols. According to "New Advent":


  ...denial of purgatory, and of indulgences and prayers for the dead. They denounced all lying as a grievous sin, refused to take oaths and considered the shedding of human blood unlawful. They consequently condemned war and the infliction of the death penalty.


are among their doctrines that contradicted roman catholic faith, so I think, that yes, they can be view as sui specie 'protoprotestants'.

Contemporary Waldenses were 'assimilated' into reformation.