The question is already answered, but I will write a bit more detail to hopefully help you understand:
You have a "For" Loop, but inside the loop you only have the lines of code:
print fc
# Add two fields to hold the results
arcpy.AddField_management (fc, "SFCount", "LONG")
arcpy.AddField_management (fc, "MFCOUNT", "LONG")
The rest of the code is not indented, so does not get included in the loop!
So your script currently works as follows:
For each FC:
print FC
add fields to FC
On the last FC in the loop only:
selection + calculate
To fix, simply indent all code after your "For" loop