Why is Christopher hiding at the end of the fifth season?

Chris is targetted specifically because he's Tony's relative.

Chris is Tony's nephew[*]. After Phil's brother is assassinated by Tony's cousin Tony B, Phil is out for blood - preferably Tony B or one of Tony's other relatives. He makes that clear in his sit-down with the Soprano crew in episode 5-12:

Phil: Anybody ever die in your arms, you c*@%sucker? A family member? Somebody you love?

Tony: No.

Phil: Well, give it time. See if I can't make that happen for you.

Johnny then signals he supports Phil's quest for vendetta:

Johnny: I want your cousin on a f*@%ing spit!

Tony: I don't know where he is.

Sil: Nobody does.

Johnny: Fine. [glances at Chris] Maybe one of your other relatives, then.

Chris: What, I gotta stand here being threatened now?

And after Tony's refuses Johnny's demands at the end of the episode, it's clear to Jersey that Phil will go after Chris, which he indeed does in the next episode by first threatening Chris's mom, then beating up Benny in an attempt to find where Chris is hiding. So it was smart of Chris to go underground, but it's worth mentioning that some people in the Jersey crew then complain that Tony only goes out of his way to protect his own blood.

As for the fact the Chris is made, I'm not quite sure how it's relevant. Phil wants "an eye for an eye" and his actions seem to be semi-sanctioned by Johnny. Made guys are whacked left and right in the show - not to mention in real life - for many reasons.

[*] [While he's considered to be Tony's nephew throughout the show, Chris is technically Carmella's cousin and Tony's distant cousin, but he's still family.]