Probably the biggest difference between most Mennonites and Baptists is that Mennonites do not participate in the military. Mennonites believe that peace is the will of God and the way our lives should be lived daily. Confession of Faith in a Mennonite Perspective states: “Led by the Spirit, and beginning in the church, we witness to all people that violence is not the will of God. We witness against all forms of violence, including war among nations, hostility among nations, hostility among races and classes, abuse of women and children, violence between men and women, abortion and capital punishment.”
Another difference would be that Mennonites believe strongly in separation of church and state, and believe that allegiance to God takes priority over allegiance to country. Baptists wouldn’t sort out the issues in this way.
Again, quoting from Confession of Faith in a Mennonite Perspective: “We believe that the church is God’s ‘holy nation’, called to give full allegiance to Christ as its head and to witness to all nations, government and society about God’s saving love. … In contrast to the church, governing authorities of the world have been instituted by God for maintaining order in societies. …As Christians we are to respect those in authority and to pray for all people, including those in government. … We may participate in government and other institutions of society only in ways that do not violate the love and holiness taught by Christ and do not compromise our loyalty to Christ.”