Tradtionally, and even in present day Ireland, Protestants were almost universally Unionists (those who supported the union with Great Britain), whilst Catholic were in favour of home rule for the whole of Ireland.
However, there were several notable Protestants who supported Home Rule, such as Wolfe Tone and Thomas Russell. The uniting of Proestants and Catholics behind Home Rule was possible as many Protestants regarded themselves as being equally Irish and Protestant. They saw no issue in their loyalty to a united Ireland and felt that it didn't compromise their religious beliefs. Similary, there were many Cathlics who opposed home rule, feeling a greater unity to the Crown.
Some Protestants supported Home Rule as they believed it was their best chance to prevent war in Ireland and to ensure the Protestant minority kept its voice in the turbulent C19 and C20 Irish political scenes.
It all comes down to priorities. Many Protestants felt able to prioritise Ireland above loyalty to the Crown, and therefore able to unite with Roman Catholics behind the Home Rule movement.