Q. How can I use a naked domain with Traffic Manager?
A. Traffic Manager works by providing a Traffic Manager DNS profile of the format <your name>.trafficmanager.net. This profile has one or more endpoints which point to targets that users of the Traffic Manager name will be redirected to based on the profile configuration such as redirection to the endpoint closest to the client. Typically an organization does not wish to publicly expose the trafficmanager.net name to the public so instead a vanity domain is used which has an alias record created that resolves to the Traffic Manager name. An example would be to create an alias (CNAME) of www in yourcompany.com which resolves to the Traffic Manager name. When a user navigates to www.yourcompany.com they will be redirected to the Traffic Manager profile which will then resolve to an endpoint.
A naked domain is where only the domain name is used, for example yourcompany.com. It is not possible to use an alias for the domain root per the RFC specification. This means it is not possible to redirect a naked domain to Traffic Manager using an alias. The best option is to instead use a URL redirect for the naked domain to www.yourcompany.com and then ensure www.yourcompany.com is an alias which resolves to the Traffic Manager name.
What would be great is if Traffic Manager could directly integrate with Azure DNS (Azure hosted DNS services) however this is not possible currently.