OK, so you were probably expecting someone like Mr. Wakem. We’d like to put forth an argument for a different sort of antagonist, in addition to the more obvious Mr. Wakem. The thing with pegging Mr. Wakem as an antagonist, though, is that it is very hard to do. This is largely because of the way this book is narrated. The narrator gives us very detailed and often sympathetic portraits of every character, even ones like Wakem, who we might be inclined to dismiss. For instance, we see that Wakem is kind to his son Philip and supports his painting. A lot of fathers would probably be a jerk to a son with a deformity in this time period.
Wakem does some pretty nasty stuff to the Tullivers. But Mr. Tulliver is arguably the cause of as many problems as Wakem, and people like Aunt Glegg often torment Tom and Maggie more than Wakem ever does. What all these potential antagonists have in common is that they all function as part of a broader society that has a lot of rules and practices that cause people serious problems. Wakem, for instance, buys the Tullivers' mill because he can and because it’s socially acceptable for him to do so. And, notably, it is society in general that causes the most problems for Maggie, namely the vicious gossip she faces after breaking-up with Stephen. (For some great quotes about the antagonistic role of society check out and "Society and Class Quotes.")
The Mill on the Floss encourages us to understand individuals. Often, individuals acting as part of a broader social network cause the most problems for the book’s protagonists and other "good" guys. Society itself not only causes problems, but it also helps to turn otherwise "good" guys bad, or at least it encourages them to behave very badly – which is not to say that someone like Wakem isn’t a jerk or isn’t responsible for his actions. The modern, and often cruelly impersonal, society of the book just helps and encourages Wakem to act like he does.