His schtick on that is that he finds it "interesting" that so many people assumed he was talking about Bush, followed by, "if the shoe fits..."
You're absolutely right. Here's exactly what he said:
KING: You said, dad was also a deeply unabashedly religious man, but he never made the mistake of wearing his faith on his sleeve to gain political advantage. Were you referring to the president?
REAGAN: You know, it's interesting.
KING: Everyone thought that.
REAGAN: I know. I wasn't watching TV much after I delivered the eulogy for a few days. But after a couple of days I started getting calls from people saying, boy you really stirred something up, didn't you? I thought, well, what? Well, you know, the stuff you said about Bush. I said, I didn't say anything about Bush, why would I mention George W. Bush in my father's eulogy?
No, no, no, no, the stuff about the religion. I thought, ha, funny, you then everybody thought I was talking about George W. Bush. And then I heard -- everybody thought I was talking about George -- but people connected with George W. Bush thought I was talking about George W. Bush. And then I began to think, maybe I was, I just didn't know it.
Now, be sure to notice that last part - "And then I began to think, maybe I was, I just didn't know it." It sounds like something a lawyer would tell him to say, doesn't it? Now, if he's ever placed under oath and questioned about it, he'll have an out. ;-)