This is just a timing issue.
The start vsperfmon /coverage /output:run.coverage command starts up vsperfmon.exe in a separate process.
Concurrently, your script goes on to run hello. If hello is a really simple program, it is possible that it executes and completes before vsperfmon.exe is running and fully initialized. If your script hits vsperfcmd /shutdown before the monitor is up and running, you will get the error you're showing.
vsperfcmd is just a controller/launcher for vsperfmon, so you can use that exclusively in your batch file:
cl /Zi hello.cpp -link /Profile
vsinstr -coverage hello.exe
vsperfcmd /start:coverage /output:run.coverage
hello
vsperfcmd /shutdown
In this case, the first call to vsperfcmd will block until the monitor is up and fully running.