To prepare the tomatoes, bring a large pot of water to a rolling boil.
Using a very sharp knife, slice a shallow X across the bottom of each tomato. Add 3 or 4 tomatoes to the boiling water and cook until the skins start to peel, about 30 - 45 seconds. Remove the tomatoes with a slotted spoon and place in a colander to drain. Repeat until all tomatoes are peeling.
Remove the tomato skins and skins. Place the remaining tomatoes in the carafe of a blender.
Using the same large pot used to boil the tomatoes, add the sugar, vinegar, and water. Bring to a boil and cook over medium heat, stirring occasionally, until the sugar is dissolved and the mixture becomes syrupy, about 5 minutes.
Pour the hot syrup over the tomatoes in the blender and add the salt and red pepper flakes.
Process until the tomatoes are broken down but still slightly chunky.
Pour the tomatoes into the same large pot and cook over low heat until the jam is thickened, about 2 hours. Stir the mixture occasionally while cooking but more often near the end of cooking.
Allow the mixture to cool completely then spoon into a large jar. Refrigerate up to 2 months.