While agreeing with you that there are some statistically terrible high profile studies (such as failure to control for cases where the subject acquired a gun explicitly because they thought someone was planning to shoot them), I think it is still true that owning a gun causally increases your likelihood of being shot.
The biggest reason is suicide. If you don't own a gun, you are much less likely to intentionally shoot yourself. The second reason is accidental shootings. If there is no gun in your house, there is practically no chance that you will accidentally shoot yourself, or that your toddler will accidentally shoot you.
Of course, the question that's really being asked is whether an individual is at greater risk of being shot intentionally by someone else if they own a gun or not. This is where the data is much thinner. This seems like a solid review article: http://www.iansa.org/system/files/Risks%20and%20Benefits%20o...
Their conclusion at the bottom of page 4 and top of page 5 is even after "controlling for illicit drug use, fights, arrests, living alone, and whether or not the home was rented", that "Yes, owning a gun increases your risk of death by gunshot". Still, I'd be interested in seeing a study that breaks apart statistics for hand guns and long guns.
(Welcome to HN!)