Since my wife went to Baylor and I've spent some time there. (Our first date was a campus sponsered sacred choral Christmas concert.) I think that she appreciated her time at Baylor and the influence was more positive than negative on her faith. I'm impressed with Baylor's desire to create a prestigious academic institution without sacrificing the school's Christian commitments. I have my doubts on the long term success. Catholic institutions have hardly been able to maintain their "catholicness" in the face of secularism (e.g. Georgetown, Loyola), and Protestant institutions have historically always bowed to secularist principles within a couple of generations (e.g. Harvard, Princeton).
Notre Dame generally has accomplished what Baylor wants to achieve -- recognized status as a top-tier university without surrendering to secularism. But Notre Dame is not without its problems - google "Notre Dame and Vagina Monologues" for details.
Read Should Baylor University aspire to become the "Protestant Notre Dame"? from ABP News.