The stories of his treatment have been horrific from some sources. Here, the explanation that Kerry says he was given is far more benign than the stories earlier this week - but they do show that he has questioned it.
When Kerry was in North Hampton, Manning's treatment was brought up - and Kerry's answer was essentially if he were being tortured, he would lead against it -
http://dailycollegian.com/2011/02/21/kerry-addresses-economy-foreign-policy-in-noho/ (Whether referring to that or something else, this article speaks of Kerry and, more aggressively, Kucinich raising questions.
This answer here is far more equivocal - and though there is a mention of concern, he is giving some credence to the reason given. (One big question is whether this is just at night as said - or if it is being done during the day to embarrass or break him - if so, there is no justification.
I can understand that Kerry, like most people in the government, do not consider him the hero that many do, but I hope that he will try to get more answers here.