Since stomach flu is an informal term anyway (not medically specific or used in a setting where you might say gastroenteritis or something like that), you can use either the definite or the indefinite article and people will understand just what you mean.
The subtlety is that when you use "the" you are implying that there is one particular virus* circulating, and your audience probably knows others who have gotten sick with the same symptoms, so your use of "the" intends to tap into the listener's knowledge of what (they or) others have experienced recently.
By contrast, "a" implies that you have acquired some virus* which affects your stomach but there are multiple such illnesses out there and you are not being specific about exactly which one you have.
In "Six facts about stomach flu" there is no article because "stomach flu" is being discussed as a general concept. When you have a/the stomach flu, you have one specific illness, and the difference between definite and indefinite article is the implication about how many such illnesses are out there within the relevant range of consideration. The article title ("six facts about...") does not imply that the author is sick at all or that the advice contained in that article is limited to any specific strain of virus*.
The bold words in the last paragraph can be read as more general guidance for when trying to decide between definite articles ("the") and indefinite articles ("a/an").
*: (or bacteria or other cause of disease).