It entirely depends on the project. For about 2/3rds of the ones that I do, I don't really need much grunt. A 50 cent microcontroller can do the job as well (sometimes better) as a full R-Pi, but at a fraction of the cost ("cost" including power usage, size, etc.). I frequently see projects using a hefty system like an R-Pi that could have been done equally well with a tiny microcontroller.

And having a full OS running means that more code is running. More code means more potential points of failure.

Of course, if your project is something that needs a larger processor or more advanced software, then what you say can be very true.

Also, if your skillset is more in line with programming larger systems than smaller ones, the development time will be shorter for you by going with a full OS.