You server/domain is probably missing some configurations that helps prove that you are not a spammer. Other mail servers have various checks in place to qualify what is spam and what is not. Many of these spam checks add details to the headers of an e-mail message which could clue you into what Hotmail may be flagging your e-mails on. I would recommend sending yourself an e-mail to a Hotmail address from your server and read through the headers (look for an option to view the message source when you have an e-mail message open).
A few examples of configurations that will cause such problems include the following:
- IP address to your mail server is deemed as being dynamically addressed. Ensure your e-mail server has a static IP address assigned to it
- Your IP address may not have a reverse DNS entry
- Your IP address and/or domain may have been flagged for spamming in the past. Consider checking the various black lists out there to ensure your domain & IP address are in good standing. A site such as http://www.blacklistalert.org/ is a good tool for this. Keep in mind that Hotmail is a very big mail service provider and likely has their own spam protection rules and lists being maintained. The headers may reveal more information about this.
- Do a check on your mail server to ensure all tests pass at http://www.mxtoolbox.com/ . All though this isn't a definitive test for Hotmail, it may point out possible problems on how your mail server was configured.
- Ensure SPF records are created for your domain.