Well the champions are not enough, just because its a Zed doesn't mean its a good Zed. In the hands of a capable player however I find that it is very difficult to punish champions like Ryze.
I guess the only thing I can say to use to counter champions like this are other safe farming champions and just play a passive lane early.
I suppose my first point was to be about not everyone is a capable player, not everyone knows the strengths their 'safe' champion possesses and so cannot use it as leverage to become the 'opsafe' champions you are talking about, for example, Vayne vs Caitlyn. Vayne is countered hard by Cait, even so if the Cait player isn't as good as the Vayne she can still lose, even though she is 'safe'
Also upon thinking it through further champions such as Caitlyn, counter aggression with their strong disengages, so I have to say that playing safe really is the only counter to champions such as these. Play a champion that can trade well with the match-up and try not to trade, at least not until they make the first move. What makes the champions 'safe' and or 'op' in standard match-ups is that they are passive and punish aggressive play. The former can be flipped however, if they turn aggressive they lose their advantage and are weakened, simply because their strength, or safety comes from their disengages that are/can be used to close the distance to make attempt some aggressive harass. If you are ever in this situation this would be the time to turn and attack, you are almost GARENteed the winning trade (unless they are fed).
If you are playing safe this should limit their ability to become fed.
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'But their jungler is ganking too much its killing us! D:' This can be countered with wards. Also with teamwork and mild coordination.
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'But they leave the lane and get fed off noobs in bot/mid/top >:U' This can be countered with hard lane shoves, punishing the lanes tower while the lane is unguarded, also you can deny them kills by alerting your team to their absence, ping multiple times if needed.
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'They are already safe champions, now they are countering me alone with items!' Lane swap! If you are top Zed and that pesky Malphite wont stop buying anything but armor, swap with midlane and punish those squishies, at the same time countering the Malphite by having him waste his starting gold on items that are useless against mages.
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'Jungler is afk and I need help against this safe champ, he's shreking me.' Call for a fellow laners support, beg if you have to, or just leave lane for a while and roam, try to get some kills and even the playing field if you are getting countered really hard.
Just some tips and tricks I've learned along the way, I hope some of this helps you with these 'safe' or 'uncounterable' champs, or maybe help you to helping others who struggle against these champions.
-edit-- Sorry if my process is unclear or messy, I am very tired, it is 5 am here, haha, so after typing this I. Am. OFF. TO. BED. SLEEP Y U SO ENTICING?!