You need to move cipherText = ""
before the start of the for loop. You're resetting it each time through the loop.
def caesar(plainText, shift):
cipherText = ""
for ch in plainText:
if ch.isalpha():
stayInAlphabet = ord(ch) + shift
if stayInAlphabet > ord('z'):
stayInAlphabet -= 26
finalLetter = chr(stayInAlphabet)
cipherText += finalLetter
print "Your ciphertext is: ", cipherText
return cipherText