It's still possible for people to find out who you really are, even if you use a pen name. For example, if you use WordPress (a popular blogging platform), someone who posts a question/comment may receive an email when their comment has been posted and/or answered. This "from" address will be whatever email address you used when setting up your WordPress site/blog (or whatever "from" email address you used when configuring one of the many contact form plugins available for WordPress, should you choose to have people ask questions via a contact form instead of commenting on your posts). Once your email address is known, it would be possible to find out who you are through various methods which I won't mention here.
Other methods that could give you away:
1) Presumably, you're selling the book online and accepting credit card payments from your customers. You'll no doubt have given your real name to the company that processes the payments (PayPal, 2Checkout, etc.). Also, some of your information may be visible to the customers during the checkout process and/or when they get their receipts. When you use PayPal, the merchant's name, email address, and phone number will appear on the receipt.
2) Someone could check your domain's WHOIS record to find your name, address, and contact information (unless you've opted for a private domain registration AND you used "vague" WHOIS data, such as an LLC with which none of your personal information is associated).
3) Your web host and ISP will have your real information, unless you used a nominee.
4) If you promote your book using paid advertising, it may be possible to identify you through your billing information.
5) Your writing style and any real-life stories that you share with your readers may allow people to deduce who you really are, particularly if they already know you personally (e.g., friends, family, or co-workers who may somehow stumble upon your book - this is, of course, assuming that your book is about your own experiences with the topic in question).
It would be difficult for your average customer to find out who you are if you have, at the very least, used private WHOIS and a pen name. They probably will not be able to access any of the "real" information that you may share with the companies involved in making your venture possible. Keep in mind, though, that discovering your identity would not be impossible, even if you used a nominee for everything.
I hope that helps you out, and I wish you luck with your business.