The obvious reasoning is Jon need to go somewhere while Lois got dressed, so Clark telling him to wait on the roof is easy. But yeah, I expect someone's going to notice and it's off to the races with the speculation as to the super-love child of Lois and Superman. Though with Jon being older, he would predate Lois and Clark's marriage by quite a bit to someone who doesn't know about Jon Kent.
I expect this secret identity/gossip angle is a slow burn story though and Bendis will torment me with it until at least next fall after Levithan.
Though the last issues of Super Sons had Jon saving Lois. I think that was pretty public.