Michelson-Morley experiments weren't the failure MIT made them out to be, just as Cold Fusion wasn't the failure MIT made it out to be
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It means "represented them as":
To "make something out to be" something else is to portray it in a certain light. If my comments make you out to be a great guy that means I am saying good things about you. If they make you out to be a jerk that means I'm not being so complimentary.