But why to bash him about it and not almost everybody else 100 and more years ago about there believes in gods (which are not inherently more real then ferries are)?

I contest your claim, and have concrete reasons to think that ferries are indeed real! ;)

Jokes aside, I partly second your claim that Sherlock Holmes methods are in fact rational. Yes, you don't get to see the whole process. Indeed, it looks like magic. But my mobile phone also looks almost like magic to me. Holmes' reasoning is evidence based. He constantly challenges the most common beliefs to see if they match with reality. He holds off on proposing solutions until he has gathered a sufficient mass of evidence. He updates his beliefs and shows no bias in how he analyzes the facts. He's maybe not a black belt bayesian, but this doesn't mean there something good to be taken from the character.