I suspect the bans are really aimed at players who use their characters' alignments as an excuse to be jerks. While it is certainly possible to create a chaotic-evil character who works well with a party, it takes a serious role-player to do so and most of the CE characters one is likely to encounter in games are solely there to screw over the rest of the party. It is also possible to create LG characters who cannot work with a group, but again, it takes a serious role-player to do so and most of the LG characters one is likely to encounter in games are not going to be a problem.
As has been mentioned CN is one of those alignments which is often used by players to create characters with no actual character who are often incapable of functioning in a party. It tends to be cyclical in my experience, players start abusing CN alignment to justify bad characters, DM bans CN (or evil or whatever, once I saw CG get so abused it was banned) out of hand, a player comes up with a reasonable CN character and talks DM into relaxing the ban for that character, players make some reasonable CN, players start abusing CN alignment to justify bad characters... .