We usually don't seem to care about that factor do we...
The EOREI doesn't really matter as long as the output is of higher quality (usable for fuel etc...) and the input energy is abundant. If there is a shortage of the energy type needed for the process (input) it will however not be profitable. From what I hear, that is one (of many) reasons why the tar sands operations in Alberta is a very bad idea. Since the process consumes lots of natural gas which is becoming increasingly short in supply in North America.
Coal is though very much abundant in many places, but please let society collapse before we go down that road. That will in the long run surely be our doom.