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Some services like Github has DDOS mitigation measures for their root/naked domain, but not other subdomain(s).

What so special about the root domain concerning the DDOS attacks?

[1] http://instantclick.io/github-pages-and-apex-domains

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You usually set up a host name for DDOS protection by having a DNS CNAME record that points to the DDOS protection provider. This lets the provider adjust the IP address (or addresses) that the domain points to.

Setting up www.domain.com to use a CNAME record is easy. It's not so easy for domain.com because once a host name has a CNAME record, it cannot have any other records, and domain.com would usually have MX and NS records to handle mail and DNS resolution.

However, CloudFlare now supports CNAME flattening which does allow this.

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