Not necessarily the more N you are the less you fit in, however the more unconventional you are, the less you fit in.
Unconventional is synonymous with eccentric, or off the center. Most people do not welcome those radically different from themselves.(Many reasons for this which we need not get into at the moment).
In order to fit in with the masses, you must be conventional, or like most people. The more intelligent folks tend to have their own vision of how they should live their lives, and therefore tend not to turn to society for inspiration as much. As a result they end up being profoundly different from most people and therefore do not fit in.
Thus the main factor associated with not fitting in is being different from others, this tends to result due to an outlook on life autonomous from that of society. Intelligence tends to be highly correlated with unconventionality. N is a big factor to intelligence, but not the main. I would argue however, strictly from a typological perspective, focus on the abstract leads to more inclinations towards intelligence than just 'N'. INTP is the only non-N dominant type who shares the fate of dominant Ns concerning alienation due to over-intelligence. In this case the intense internal focus compensates for a lack of Intuition.
Pure mercury's post seems to set an example that it is possible to arrive at the same point as many of us here have, namely alienation due to being profoundly different from most. I suspect the common root in all these cases, once again, is intelligence which leads to autonomy of thought, that in effect places one in a position where he does not rely on society for concoction of his identity, and in most cases becomes profoundly different from most members of society.
So, to put it this way, the more intelligent you are, the less likely you are to be unconventional. And the more unconventional you are, the less likely you are to fit in.
Another reason why intelligent people tend to have difficulty connecting with others is because their outlook on life tends to derive from within. Obviously, if you derive your sense of self from within than from without, you will encounter less people similar to yourself.
Naturally we gravitate towards those we have much in common with. The more open-minded of us can come to understand and accept those very different from us, but embracing them on a deeper level shall be very difficult.
Thus in conclusion, the more intelligent people do not fit in with society because they are different from most people. They also tend to have difficulty establishing relationships with others because they do not find many people who have a similar outlook on life to that of their own.