There are some good counter measures. CloudFlare, the CDN that I'm using for my site http://gitignore.io helps mitigate DDoS's [1]. Github also took a good step by separating the source code domain github.com from the pages domain github.io [2]. I agree that tomorrow Atlassian could suffer a DDoS attack but I feel like since they are a more mature company, they have a lot more experience dealing with that type of attack.
There comes a point where there isn't enough bandwidth you can buy...Reflection and amplification attacks can, very quickly, generate in the 100's of Gbps worth of traffic. IT simply isn't economical to keep that much bandwidth at hand all the time.
Tomorrow Bitbucket can get under the same attack.