What does he mean by what? The "something else" he said? Hard to answer that without key information -- you know, like, what the hell he actually said?
But that's irrelevant. Why are you breaking up with him over e-mail? Not cool. No wonder he didn't reply to it. I wouldn't, either. What, the telegraph office was closed?
E-mail's great for "How's your day?" and "Can you pick up some Febreze on the way home?", but not so great for "I don't love you anymore" or "I'm pregnant and it's not yours." Unless you live far apart, important news needs to be given face to face. If it's a distance relationship and face-to-face isn't possible, a phone call is better than an e-mail, and Skype is better than a regular phone call.
Yeah, I know, it's harder that way, but too bad. It's a respect thing. You're delivering news that will have a negative emotional impact on the receiver. You can lessen the blow and show that you give a damn about his feelings by doing it in person (or as close to in-person as you can get.)
Think about it. Would you like to get dumped via e-mail? Or fired? Or told that a family member had passed away? Or that "Jersey Shore" got cancelled?
Now you get to break up with him again. Do it in person this time. No pigeons. No skywriting. No messages in bottles. Grow a pair and do the right thing.