Greetings! The Roman Catholic Church and Protestant churchs such as Baptists are quite different in perspective.  There are also two branches of Baptists, the Southern Evangelical and the more conservative Baptist. 

The Roman Catholic Church is set up with the priests that report to a Bishop that reports to the Holy See, the Pope.  The services are quite different as well.  In order for the parishioners to receive communion, they must first confess to the priest their sins.  In the Catholic faith, parishioners look to the priests as intermediaries to Christ and God. There is not a direct link.  They also have various religious orders.  Priests cannot marry and at the current time, only men can become priests, although they are allowing women to do some lay work.  The services are also different as well.  Some of the rituals actually hark back to pagan practices, such as the censor.  Baptism is generally done when the babies are quite young with a ceremony to welcome them into the Church around age 7-9 with confirmation later in teen years after they have completed the requirements set out in CCD classes (similiar to Sunday School).  There is also the worship of various saints, although this is not in the context of religious expression within the church service.  At Easter, communicants will do the 12 stations of Christ, which celebrate the cruxificion.  In churchs, instead of a plain cross, they have Christ on the cruxificion cross.  Those are the outward differences.

With the Baptists, depending upon which branch you subscribe to, ministers can be male or female, and of course, can marry.  Although there may be a baptism as a baby, which doesn't necessarily have to be shortly after birth, the main baptism is done when the parishioner decides to become a member of the church.  The members believe that in order to go to Heaven they must be "saved" and undergo baptism in water, like John the Baptist did to Jesus.  This is especially done in the Southern Evangelical branch in which the churchs have pools, generally behind the choir loft and are done in special ceremonies, generally separate from the usual Sunday observance.  The Catholic Church has services on Saturdays and Sundays and many offer morning devotions during the week.  The Baptists tend to have services on Sundays with a Wednesday night prayer meeting.  The services are also streamlined without all the kneeling and gentiflexing of the Catholic church.  The choir is very much a part of the service.  Although the pastor acts as a guide to his/her parisionshers, instead of acting as an intermediary to speak with Christ or God, the parishioners have a direct link.  There is no absolution for sins such as in the Catholic church.  Also prayers are different.  In the Catholic Church, the Our Father and Hail Mary is done as part of ritual.  In the protestant faiths, it is The Lord's Prayer with "debts and debtors" instead of "tresspasses"  The prayer also ends a bit differently.  Unlike the Catholic Church, the Baptists (especially the Evangelicals) are asked to go out to spread the Word of the Gospel.  Indeed, many times, the pastor will ask if anybody wishes to be saved to come forward at the end of the service.  In order for the members of the Baptists to go to heaven, they believe that they have to be baptisted into the spirit of Christ in order to go to heavenj. 

These are the basic differences, but there are many liturgical differences, differences in services, etc.  Hope this helps.