It really depends on the use case and the applications, some times it is an overkill to use a system like the RaspberyPi fo r just monitoring some sensors or controlling a relay switch. Especially when it comes to price, size and power consumption, microcontrollers are the only answer. System on a Chip devices can make great gateways for microcontrollers and supplement functionality by providing e.g., data processing, secure communication, etc.
For a large percentage of the vast number of other uses of microcontrollers - no, most definitely not.
A microcontroller has a number of properties things like the raspberry pi don't have: they cost a hell of a lot less (the micros I've used cost between about $0.50 and $3 each when buying about 10 at a time), have a much smaller physical footprint (SMD micros are anything from a few mm^2 to a cm^2 or so) and require very very low amounts of power.
