From the casinos' point of view, some banking methods are more beneficial than others. Understandably, casinos try to channel the players to use these methods.
The most common way is to remove handling fees. However, casinos also offer additional bonuses for people using the preferred banking methods. The bonus percentages aren't big, but they're sometimes added on top of your standard deposit bonus.
Banking method bonuses aren't as common as they were a couple of years ago. Also the set of payment methods available in online casinos have become more similar.