Brooks is a polarizing actor, to be sure. I attribute the eccentricities in his acting to three things:
One is the fact that he played such a complex, multifaceted character. There were a lot of different sides to Sisko (leader, father, religious icon) and he brought something different to all of them while still staying true to the character. That's a tricky balance to pull off and not come off as bipolar - a criticism often leveled at Kate Mulgrew. I think he succeeded for the most part. I'd also add that Brooks benefited from good, consistent writing for the character.
The second is that he was first and foremost a stage actor, and even after seven years that heightened sense of theatricality remained. (Patrick Stewart was also guilty of this, to a smaller degree.) I've directed stage actors in film projects and it takes a lot of work to bring them down to the level of intimacy required for TV acting. There were definitely moments where Brooks needed to be reined in more.
Third is his real-life eccentric nature. In interviews, he comes across as extremely intelligent but more than a bit "out there". It's a testament to his acting (and the writing and directing) that the character comes off as real and grounded.