Remove lines that contain certain string

You could simply not include the line into the new file instead of doing replace.

for line in infile :
     if 'bad' not in line and 'naughty' not in line:
            newopen.write(line)

You can make your code simpler and more readable like this

bad_words = ['bad', 'naughty']

with open('oldfile.txt') as oldfile, open('newfile.txt', 'w') as newfile:
    for line in oldfile:
        if not any(bad_word in line for bad_word in bad_words):
            newfile.write(line)

using a Context Manager and any.