No-one here is denying that Nape is a top tier threat, and I personally hate having to deal with it (Thankfully though my teams aren't weak to it, I always pile on two are three checks that rarely if ever include Starmie). What we (or at least me), are denying is that Nape is worthy of S rank. In every tier the top mons are inevitably the ones that can perform the most roles and do the maximum for their team. Nape......attacks and does nothing else (asides from a utility Mach Punch but that's getting rarer these days). Furthermore, as the wise McMeghan pointed out, Nape is the polar opposite of durable and even resisted hits are going to take their toll on you. People (Frenchmen) say U-Turn is amazing to grab momentum but it forces you to come back in on hazards again and take even more damage, and it offers a free switch - in to Flying types (Gyarados, Dragonite, the terror that is LO Aerodactyl, etc, along with Nidoqueen and other Resists that suddenly threaten to set-up).
Speaking of that, though Nape has no counters, the number of switch - ins and lures it has is pretty extensive: ScarfTar, Chople Tran, Starmie, Occa Jirachi, Dragonite, variants of Gliscor, Defensive Zapdos, Scarf Rotom-A, Gengar, Gyarados, Scarf Flygon, Hippowdon, Swampert and of course LO Aerodactyl. Though none of these will win against a well played Nape with adequate support on their own, two or three of them can at least keep Nape from devastating them (or at least make sure that it doesn't end in Nape sweeping). Combine with the fact all these mons are pretty easy to slap onto a team and you have a meta where Nape doesn't exactly run rampant, and is not S (it is a killer mon though, and can get past all its counters assuming it lives that long, so mid-high A+ seems fair).
Edit: after reading Ojama and Go10 's posts more thoroughly, it seems more like they're saying that Nape is basically unbeatable, guarantees wins for mindless U-Turn spam, and generally unbalances the metagame. Not exactly serious on this, but I just wanna know: how would people feel about an Infernape suspect?