Use the article when it is countable. Soup can be used in either a countable or non-countable sense.
If you refer to soup generically, such as the type of liquid in your bowl, it is non-countable, so you would say "this is good soup". Similarly, if you are talking about a restaurant that does a good job preparing soup, you might say "they make good soup".
It becomes countable in some special cases. For example, you're judging different soups in a taste-off. If one of the soups is good, you might say "this is a good soup"; it's countable in the sense that it is one type of soup in a collection of different types of soups.
People sometimes use "a soup" when referring to a standard serving of soup. For example, when getting a can of soup from a vending machine, or ordering a serving of soup in a restaurant ("I'll have a soup").
However, you wouldn't typically refer to that as "a good soup" if it was good. "A good soup" uses "good" in the sense of a category of soup, which is a different sense from a unitized portion of soup. The article doesn't do double-duty. If you got a unitized portion of soup and it was good, you would typically say "this is good soup".
If the quality of the soup is hit-or-miss and today's serving happened to be good, you might say "this is a good soup", but the reason would be similar to the taste-off case -- it's one example of soup from the good category, rather than being related to the unitized serving.
The use of the article is based on the context, whether the point of the sentence is to convey something about soup in a countable or non-countable sense.