They also oddly attacked Kerry's comments that the Bible's words would lead you to fight climate change. They attacked that he was Christian, that he ever read the Bible, and that the Bible could possibly be read to suggest that - apparently not understanding what being a good sheperd of the earth means.
However, they attack anyone who does not buy into their "Islamofascist" nonsense AND they attack Kerry just for who he is. I doubt Kerry or anyone in the administration did not know that this would be their reaction.
Then consider that Kerry would not even have been expected to attend the ceremony given that this was not a direct report and he is so busy. In addition, attending did not mean that he had to give a speech like this rather than just praising the new appointee. So, why given everything he is working on did he write and give this speech?
I suspect that the audience was not really the State Department or the US public, but rather the various Muslim diplomats that Kerry needs to work with to succeed in helping Obama get the Middle East to work with him against terrorists - including ISIS. I hope that, even if it is just their diplomats, that this message goes to the Middle East.
In addition, as Yvonne noted, it really is of a piece with his Pepperdine speech and, as he mentioned himself, the Yale speech. Though it would have stunned people had it been said in 2004, it is very likely that Kerry is among the most informed Senators on religion, whether Christianity or world religions. Religion and diplomacy are both at the core of who he is. As to the attacks, he has been attacked by the right since 1971, he knows who he is and is clearly not going to change to appease haters - especially when he is really out of politics.