It could be any number of reason that emails are going to the spam folders, but its worth doing the following
- Add SPF and DKIM DNS records in order to certify that the e-mails are legitimate.
- Change the default “from” e-mail address and “from name” fields.
- Change the wording in both the email subject and content.
You could try a 3rd party mail service like mandrill to send emails, they allow up to 12,000 emails a month for free.
Email confirmation is a necessary step to prevent spammers, even better is when the user has to activate their account by clicking a link in the email they received.