Use generator expressions, the best way I think.
for line in (line for line in x if not line.startswith('?')):
DO_STUFF
Or your way:
for line in x:
if line.startswith("?"):
continue
DO_STUFF
Or:
for line in x:
if not line.startswith("?"):
DO_STUFF
It is really up to your programming style. I prefer the first one, but maybe second one seems simplier. But I don’t really like third one because of a lot of indentation.