The Episcopal church in Scotland was very powerful until the mid-18th century when it was basically driven out of its position as it tended to be very supportive of Jacobitism.

The Presbyterians then really came to the fore. I grew up in Scotland, in the Episcopal "heartland", let's just say they are pretty insignificant nowadays.

The Scottish settlers in Ulster tended to come from areas where Presbyterianism was very strong even before the 18th century.
I'd also like to point out that there were undoubtedly plenty of Scottish Catholics who settled in Ulster (just consider the MacDonnels of Antrim) too.
Also, some of the native Irish converted to Protestantism.