The Christian religion can be (very roughly speaking) broken down into two categories: Catholicism, Protestantism. Presbyterians are one type of Protestant. So you can't really compare the two. You can compare Presbyterians to other types of Protestants (Lutherans, Methodists, Baptists, etc).
After Luther's 95 Theses in 1517, people who left the Roman church for the Reformed church were called Protestants, because they "protested" against the scripturalALractices of the RC church.
The Presbyterian denomination was formed by John Knox as one of many Reform, or Protestant, denominations.
Presbyterians are Protestants, but not all Protestants are Presbyterians.
Presbyterianism is a lot like Catholicism except for the doctrine. It's protestant doctrine, but you sit still and shut up the whole service long. Any Christian who is not Catholic is a protestant, no matter what those self-absorbed Baptists say.
Who cares? You both believe that some guy who lived in the middle east 2000 years ago is your god. What are you guys going to do, fight it out? I hope so: like in Ireland.