I realize this question incites speculation, but I'm trying to compile the most logical conclusion possible based off in-game lore.
After playing through the game and playing then hidden glitch level,
it seems fairly safe to say that Charlie Matherson Jr is Slender. This is for a few reasons:
Firstly,
You run at the Charlie Matherson Jr. poster to enter the glitch level, where it says "I'm lost, can you find me?". You find Slender, and he says "I like you let's play a game". Not only is this childish, but it associates the missing poster with Slender.
Also,
When you die in the glitch level, they place Charlie Matherson Jr's face directly on top of Slender's missing face, implying that is his face.
On those grounds alone it seems fairly likely. However there are a few snags:
After you find CR burning in the radio building and get attacked by that bizarre blue creature, you find the "?" note that details how CR was trying to help Mr. Matherson find his missing son. In the note it mentions that Mr. Matherson is dead, but finding his son would help him be at peace. This means that Mr. Matherson might be slender, but he could also be that weird blue creature.
But the biggest problem is that
you can actually find Charlie Matherson Jr. In the prologue, after crossing the bridge, in an abandoned building. Charlie Matherson Jr is crying inside, and if you approach him, he vanishes. There is proof that is Charlie, because you get the "Cry Baby" achievement for interrupting Charlie's crying 3 times.
Now, of course, he vanishes. So it could be a ghost, or just Slender in a different form. After all,
Kate is crying at the end of then game, but immediately becomes the proxy when you approach her.
Have I missed anything that gives a more definite answer? It seems possible that it could be either of them.
11 Answer
Playing through the game, it is revealed that
Charlie is actually the blue creature at the end of the game,
he can't be slender. It also is less likely to be his dad because he says in a note that Charlie is gone but he is looking for him. Considering Slender is primarily focused on kids, this makes perfect sense.
