python check output find command not working

You would need to pass a single string exactly as you would from your shell if you want to use a wildcard:

from subprocess import check_output
cmd = 'find /media/pi/*/config.txt'
out = check_output(cmd,shell=True)

You don't actually need subprocess at all, glob will do what you want:

from glob import glob 
files =  glob('/media/pi/*/config.txt')

Since you are using the shell=True you can use the following:

from subprocess import check_output
cmd = 'cd /media/pi && find . -iname config.txt'
out = check_output(cmd, shell=True) 

Try to avoid use of wildcards if possible, and just change your current working directory before searching for your target file.