If they know you're tough, shopkeepers often give in without a fight. But if you're small-time, they'll need a little extra convincing (in the form of smashed furniture and missing teeth) before they'll cave. But be sure to only abuse them to a certain point, or they'll start fighting back in earnest and you won't get a cent out of them.
Getting them to pony up is only half the battle, though. Each business is protected by color-coded thugs from the Tattaglia, Cuneo, Stracci and Barzini families, and there's usually a small army of the bastards protecting whatever illicit nonsense is going on in the back. Fighting through these bits can be tough, although once you've memorized the four or five "back room" layouts, they fall into predictable patterns. Even if you're successful, though, it'll worsen your "vendetta" with the crime family in question, eventually leading to a mob war that can cost you other businesses.