I'm sorry too... getting dumped sucks, no matter how it happens.
Given that you weren't together long and it doesn't sound as though you spent a ton of time together during those 3 months, I don't share some of the other ladies' outrage over an email break-up. For a longer-term relationship where you spend significant portions of the week together and your lives are more intertwined, then definitely, in-person is more appropriate, IMO. At least his message was honest and respectful, and he doesn't seem like a jerk. I agree with Curly Sara's suggestion of a brief, polite response wishing him well, since it appears he put some thought into his correspondence to you.
3b/c and outta control