A few things of note.
If you are going to be checking membership against a list over and over, I would use a set instead of a list.
stopwords.words('english')
returns a list of lowercase stop words. It is quite likely that your source has capital letters in it and is not matching for that reason.You aren't reading the file properly, you are checking over the file object not a list of the words split by spaces.
Putting it all together:
import nltk
from nltk.corpus import stopwords
word_list = open("xxx.y.txt", "r")
stops = set(stopwords.words('english'))
for line in word_list:
for w in line.split():
if w.lower() not in stops:
print w