I can imagine that whether or not cilantro tastes like soap, whether or not you love the smell of books, similar allergies, and if you can stand to eat spicy foods goes a long way toward the likelihood of friendship. There are bound to be social factors, geographic factors, and other factors. This study is just pointing out that friends are likely to be more similar in certain ways than people who aren't friends. Don't jump to too many conclusions on just the summary article about the study.
> They examined [polymorphisms from] 2,000 people and correlated their similarity within the roughly 1,400 pairs of friends within the group.
>the Framingham data is relatively homogeneous in terms of ethnicity, consisting largely of people of European descent.
The population they studied seems very close knit and ethnically homogeneous, and the study's inferences are conditioned on this sort of population.
Presumably the consistent background genetics of the population allowed them to control for larger genetic differences and detect the subtle differences correlated with friendships in the group.
I would be surprised if the observed effect held up in a more cosmopolitan population where other stronger factors, both genetic and sociocultural, have more of influence in the formation of friendships. And, as others have noted, the observed effect was real, but very small.