Quoting from Ant Drewery:
Like its predecessor Windows Mobile 2003, WM 5.0 lacks a wide selection of trusted root certificates installed by default. If you’re using a non-maintream or self-issued certificate you’ll need to do a little extra configuration to get ActiveSync working over the air. With WM 2003 there was a tool to disable certificate checking but it’s not compatible with WM 5.0. Instead follow these instructions:
In Internet Explorer go to your Outlook Web Access site and ensure your certificate is installed. To check the name of it you can double click on the padlock icon in the bottom right of the browser.
Now in the Internet Options in IE go to the Content tab and click the Certificates button.
Now go to the Trusted Root Certificate Authorities and find your certificate.
Select the certificate and click on the Export button. Follow the wizard and select ‘DER Encoded Binary x.509' when prompted.
Choose a suitable file name and finish the wizard.
You’ll now need to copy the exported certificate to your PocketPC device either via a memory card or by USB. Once it’s on your PPC simply tap it with the stylus and follow the prompts to install it.
With the certificate successfully installed you should be able to synchronise over the air.