Complex sentence: In confessional matters he was for a union of all Protestants; though a Zwinglian, his readiness to compromise with the advocates of consubstantiation gave him trouble with the hard-line Zwinglians.
Split into simpler sentences: In confessional matters he was for a union of all Protestants. Although a Zwinglian, his readiness to compromise with the advocates of consubstantiation gave him trouble with the hard-line Zwinglians.