First, MongoDB is not a key-value store, it is document store. Industry scale sites use NoSQL for parts of their stack to address a specific problem that a NoSQL data-store solves better than relational databases for example Redis is optimized for performance under real-time data workloads and hence it is better fit for storing real-time data than MySQL. Relational databases are still heavily used as main data-stores.
The bottom-line is relational databases are fine in most cases. Use other technologies when you want to address relational database shortcomings and use tools specific to the problem. Don't preoptimize. Tackle issues as they come.