Writing a python module to run Infernal on a list of fasta files
I think what you want to do is:

import subprocess
import os 
import glob

genomes = glob.glob(os.path.join("/path/to/genomes/", "*.fa"))

for gfile in genomes:
    subprocess.Popen(args=["cmsearch", "/path/to/covariancemodel/", gfile], shell=False)


each pass through the for loop will take a one of the genome files and pass it into the cmsearch command. 

Note: 

1) glob.glob returns a list so no need to cast it again - https://docs.python.org/2/library/glob.html