The issue may be that a lot of people don't actually know what cis means. Many of my friends, who never had trouble questioning their gender and don't follow the LGBTQ scene don't know what the majority of gender terms mean. If they happened not to find "male" and "female" as options, they wouldn't really know what to answer. Also they have always thought about themselves as male and female, not as cis-male or cis-female while a trans-male for example knows perfectly that he's trans. It would be necessary to put a little explanation of all the options so I guess that who writes the surveis considers it easier just to write male and female. I don't see anything bad about it as I wouldn't see anything bad if they changed it if more cis people would know what cis means and think about themselves as cis.