First of all, you don't have to initialize variables in Python. It will usually create them as needed. Just this code should be sufficient:
import random
with open('questions.txt', 'r') as question_file:
questions = [line.strip() for line in question_file]
with open('answers.txt', 'r') as answer_file:
answers = [line.strip() for line in answer_file]
# Make a list of tuples: [(q0, a0), (q1, a1), ...]
trivia = zip(questions, answers)
# Shuffle it in place
random.shuffle(trivia)
# Then iterate over it
for question, answer in trivia:
# play the game
pass
Hopefully you can see how this could be easily incorporated into your main. By the way, you can use:
if __name__ == '__main__':
# code here
pass
to define code that should run if your program is invoked on the command line. You also don't need to explicitly close
files, as the with statement does this automatically.