There is no specific reason. I don't think you understand who the Flash is. The rogues hate Flash because they are bad guys and he's the good guy. The Rogues aren't like Batman villains. They actually love having the Flash around. Think of them more like pirates. They just steal money and don't kill people.
This is what makes the Flash kind of a neat little character.
Also, they've already explained why the rogues look the way they do now.
My advice is don't worry yourself about how specific characters met. It doesn't matter. Like every Marvel and DC character, over the next 5-10 years of real time every thing you read today will be retconned or discarded a half-dozen times anyway. Just know that Flash is the good guy and his enemies are bad guys. Usually. They don't like each other and they fight about it. Except for sometimes when they don't.
As of THE FLASH #1, Barry is 5 years into his career.
I've never been much of a THE FLASH reader until now, and I loved the book until Manapaul left.