William Penn called his colony a "holy experiment." Why did William Penn believe his colony was different from the other English colonies?

Any answer to this question must begin by recognizing the uniqueness of Penn's status as a Quaker among the founders of the English colonies.
The ideals of the Society of Friends were based on tolerance and non-violence. In England, and in Europe as a whole, people had fought each other for centuries because of religious differences. Penn and his fellow Quakers believed in the toleration and acceptance of all denominations of Christianity and of all religions in general. In this they were different from the other dissenting sects in England and nearly everyone else at that time.
The Puritans were dissenters as well from the Established Church, the Church of England, in their case because they did not believe the Church had "purified" itself sufficiently of the vestiges of Roman Catholicism. Yet when the Puritans established themselves as leaders of the Massachusetts colony, they were intolerant of other denominations, just as the Established Church had been intolerant of them. Penn wished to avoid this sort of thing, welcoming all faiths and discriminating against no one in his "Holy Experiment."
Penn's attitude to the Native Americans was also different from that of the English colonists elsewhere. Again, unlike the New Englanders, Penn did not regard the American Indians as "merciless savages" but attempted to deal with them fairly and to abide by agreements to purchase only limited areas of land from them, as in the "Walking Treaty." As Voltaire was famously to comment later, Penn's treaty was the only one in colonial America:

that was never sworn to [because the Quakers did not believe in making oaths] and never broken.