Freedom of speech only says the government can't stop your speech. It doesn't say that private organizations have to provide you a platform. Youtube also has freedom of speech. They have the freedom to filter and compile videos that they like and only show those. It's also not youtube's responsibility to optimize their site for helping the NSA to track terrorists.
If I create a website that allows people to upload videos, it's perfectly fine for me to filter those videos and only show the ones I like. It's my website after all, I am allowed to control what is on it.