There are plenty of things that the president would never get access to because it doesn't ultimately matter what your clearance level is if you can't make a good argument for why you would need to know the information that you're inquiring about. It easily could have been long decided that presidents don't need to know about aliens.
That being said, the idea that aliens have visited Earth, and only certain US government personnel know about it is stupid, in my opinion.
I use Google... A lot... >____>