Syracuse also maintains ties to the Methodist Church.
Not MT programs, but many people may not realize that these two top-ranked schools are Methodist:
Duke
Emory
Other top 20 schools with religious affiliations include Notre Dame and Georgetown (Catholic).
The stats below are from Campus Corner for counts of colleges with religious affiliations (not sure how accurate they are):
Catholic 270
Baptist and Southern Baptist 101
Methodist 99
Presbyterian 59
Jewish 34
Lutheran 35
Church of Christ 39
Disciples of Christ 18
Other Protestant 26
Interdemoninational 30
This list is not completely inclusive of all denominations.