That is not true. It was one ticket, but required a domestic flight within Turkey (Ankara -> Antalya) which is why the visa was required.
But that is really besides the point. The point is about the crap the Turkish airport authorities can arbitrarily decide to put you through with little recourse if they don't like your last name or kippa. It was a direct answer to the question about the safety of transiting in Turkey.
While it is correct that an internal Ankara->Antalya flight would have required a visa, I still doubt it was a single ticket.
When one has no proper documentation/visa one can get into similar problems in almost any country, including the US. It should also be pointed out that with the possible exception of the ESB-AYT leg, it is highly unlikely that any of the legs were on Turkish Airlines.
Question wasn't about the country, but rather about the AIRPORT. While IST Ataturk Airport is not an ideal airport to transit, as it is huge, old, with bad signs, there is absolutely no security problem there.
In today's day and age, transiting for international flights (especially involving travel to/from the US or TLV) isn't a pleasant experience. And I have noted elsewhere the problem with Gözen security not emphasizing proper use of deodorant with their employees. But I wouldn't make that a reason not to transit via IST.