Did the Protestant Reformation ultimately make Europe a better place or did it cause harm to Europe?

Untold harm.

It started over a century of vicious religious wars in Europe that killed literally millions of people,held back technological advances,and swallowed up national revenues and resources that could have been better used combating Ottoman Turk expansion and on internal social and infrastructure improvements.

Ideas that extreme Protestantism - such as the Protectorate regime in Britain in the mid 17th century - brought Europe "into the modern era" are entirely false.After all the Enlightenment started in France - a Catholic country.

The Protestant Reformation was good because it put in place the structures and beliefs that would define the continent and bring it into the modern era.