My jam was delicious but it had lots of tomato skins that didn't break down. Would you suggest peeling tomatoes first?

I made this according to the recipe (almost -- I reduced the sugar substatially) with skins. We had no problem with them. Maybe the variety of tomato makes a difference.

Thanks so much to everyone for all you helpful answers. I'm going to use my food mill to remove the skins. LOVE this jam

If you want to keep the depth of flavor from the skins, but not have them in chunks, perhaps peel first then puree them and add back to the jam?

If you're going to do this a lot, or you make lots of tomato sauce, etc., you really would benefit by getting one of these: http://www.amazon.com/Victorio-VKP250-Model-Strainer-Sauce/dp/B001I7FP54

I prefer the food mill route--peeling tomatoes can get tiresome, and I also want to extract all the flavor from the tomato--skins included--before I toss them. Using a food mill after the tomato jam is done is a great way to get rid of the skins and is pretty easy to boot.

For others who might find it helpful, Amanda's response to this question on the recipe page was: "The tomato slices and skins should have stayed mostly intact, so it sounds like yours turned out right. If you don't like the tomato skins, you can either peel the tomatoes before cooking or simply cut the tomatoes into chunks so the skins are minimized."

...either peel them first or use your food mill.

You can easily peel tomatoes but a food mill would work as well for separating skin.