Well, the brain wasn't really considered back then, other than it was divided up into areas. i.e. some areas contained memory, some contained emotion etc...We have to consider the context of this half-c0cked theory. At the time it was THE new thing. Everything's in context. I feel sure that in years to come, DNA and fingerprinting will be looked at skeptically. But at the moment, it's considered 99% exact.
Of course, the obvious danger with Lombrosian theory of Criminality, was to just look at someone's shape of the skull or "eyes being close together" (ever heard anyone say that...) is that you're labelling someone a criminal without an actual offence or trial. And as we know, for law to be broken we have to have 2 things: the actus reus (the criminal act) and mens rea (the guilty mind). Lombroso once pointed a guy walking down the street and said "HE is a criminal...not legally, but anthrapologically". Very dangerous stuff.
BUT what was good about Lombroso was he was the first to look at the innate aspect of criminality. Which we use today; neurology, chemistry, A.D.D. etc...