Why was Sir Simon chained and who chained him?

Sir Simon was chained because he killed his wife. We can piece this together from the evidence in the story. First, Sir Simon tells Virginia that his wife's brothers left him to starve in retaliation for murdering their sister. He says:

I don't think it was very nice of her brothers to starve me to death, though I did kill her.

Later, after Virginia prays that Sir Simon be released to die and go to his grave in peace, she takes her family to a room where he was chained up just out of reach of food and water:

...a little low room, with a vaulted ceiling, and one tiny grated window. Imbedded in the wall was a huge iron ring, and chained to it was a gaunt skeleton, that was stretched out at full length on the stone floor, and seemed to be trying to grasp with its long fleshless fingers an old-fashioned trencher and ewer, that were placed just out of its reach. The jug had evidently been once filled with water, as it was covered inside with green mould. There was nothing on the trencher but a pile of dust.

From this, we can can determine that the brothers chained Sir Simon up to die of starvation for murdering their sister, tantalizing him with the food he couldn't eat. Now, however, his ordeal is over.