Complex sentence: With the favor of the Tokugawa the temple prospered but, at least in the first years since foundation, it was just the Tokugawa family temple, and the sole funeral temple of the Tokugawa was still Zōjō-ji, where the second shogun Hidetada rests.
Split into simpler sentences: With the favor of the Tokugawa, the temple prospered but, at least in the first years since foundation, it was just the Tokugawa family temple, not its funeral one. The sole funeral temple of the Tokugawa was Zōjō-ji, where the second shogun Hidetada rests.