There are two complementary skills that are very useful in query tuning. One is the ability to read and interpret execution plans. The second is knowing a bit about how the query optimizer works to translate SQL text into an execution plan.
Putting the two things together can help us spot times when an expected optimization was not applied, resulting in an execution plan that is not as efficient as it could be.
The lack of documentation around exactly which optimizations SQL Server can apply (and in what circumstances) means that a lot of this comes down to experience, however.