Nick's statement refers to tolerance of conduct, . . . but the quotation you speak of has a deeper meaning than one may suspect. First, it is important to put the comment from Nick's father in further context in order to delve further:
I am still a little afraid of missing something if I forget that, as my father snobbishly suggested, and I snobbishly repeat, a sense of the fundamental decencies is parcelled out unequally at birth. (1)
Upon first glance, the reader may mistakenly think that the term "fundamental decencies" refers to money. In fact, perhaps it did refer to riches in Nick's mind when he was younger and more naive, . . . before Nick lived in West Egg on Long Island. However, the real meaning behind the term "fundamental decencies" is revealed just a few sentences later:
And, after boasting this way of my tolerance, I come to the admission that it has a limit. Conduct may be founded on the hard rock or the wet marshes, but after a certain point I don't care what it's founded on. When I came back from the East last autumn I felt that I wanted the world to be in uniform and at a sort of moral attention forever; I wanted no more riotous excursions with privileged glimpses into the human heart. (2)
Point blank, Nick tells us here that "fundamental decencies" refers to "conduct" between people. And although we may have been led to believe that the rich seem to have the upper hand in this arena, Nick is here to tell the reader that that is most certainly not the case. Ironically, he tells us this before the story even begins! However, by the end, the reader will realize the despicable conduct of these East Eggers and West Eggers and have no doubt about the reason why Nick flees back to the Midwest, . . . for he gave us the reason on the very first two pages.