You *can* and many people *do,* however, don't stir up any issues or get into any legal trouble.
I wouldn't put only my initials on any domains that are very valuable, in the rare case that the registrar wants you to provide legal documentation that what you've provided is your real name, where if you've aggravated the rep or they're in a bad mood, they can take "John D" as not being "John Doe," and you can risk losing your domain. It is very rare that all of the factors will be against you, but hey, it happens.
My opinion: It's up to you, I personally have never heard of anyone getting into any trouble or issues for doing this, and after whoising many people's domains on here, I've found that the majority of them use their initials.
I also don't know of a policy that says you can't, but I do know of a policy that states that you need to provide your "real" name. John's "real" name is still John, but as it requires a last name for registration, "John D" is not "John Doe's" real name, even if "John Doe" is "John D Doe," as in their database first, middle, and last names are in separate columns. In such cases where your middle initial is a single letter (when has this happened?) it can be arguable.
Also, don't take anything I say as facts, as I've only been domaining for a few months and am an amateur.
