i have been playing mk 9 for the last month i would say, and this is the first mk game i have ever played.. when i choose characters online in a fight, i always hide cursor, wait for them to select a character and find a character that i feel can counter them... (I.E  subzero to counter liu kang because he can set an ice clone to counter air kick attacks and slow his kombos down with his freezing abillities).. does anyone else believe in this and if so what character do you use to counter other characters 

Smoke counters Noob with his shake thing move.

It's not a bad idea but usually it tends to be a smarter idea to just pick a character that you are comfortable with. That being said, if you play well with multiple characters you might as well pick the best match up possible.

 I'm not great. Only a 50/50 record. But I find the matches I win have little to do with who I'm playing as (or their specials), and more to do with how well I'm using the basics properly (zoning, meter usage and knowing what the normals do for your character and how to exploit them). The matches I lose are usually because I fail to punish or became WAY too predictable with my specials. So don't spam any unsafe moves. 
But I think Cmdc00kie is right in that winning is more likely when you're not a jack-of-all-trades. So master a smaller number of dudes. For me, Smoke is my best. If buddy's winning handily while I have Smoke out, odds are he'll whoop me no matter who I'm fighting with. 

But to your question (and someone help me out if they know better):
- Sometimes I'll come across a Kung Lao, Liu Kang or Johnny Cage who chew my ninjas up with rush down. For those two I break out Sonya (her uppercut is one of (if not) the best, and her military stance moves catch most people off guard... the low one, forward+1 is her best low move). 
- If I've got a pesky ninja, I'll usually break out Sub Zero (for his 2,2,2 and ice-clone) or Smoke (for his CRAZY teleport and projectile punishing).
- If I'm fighting a Sub Zero, I'll just about always pick Scorpion. It's more habit, really, but his ground flames will easily punish a Sub Zero who needs his clone for room. Just don't trade with ice ball.
- Quan Chi?... Honestly no idea. I've neglected this dude, and should probably practice more with him. I imagine Kung Lao or Raiden would be a good match up here (do to mobility and unpredictability). I could use some tips here, myself. All I know is be ready to block and punish his garbage teleport.
- If you're fighting Sheeva JUMP. If you're fighting Kabal DON'T JUMP. And if you're fighting someone who thinks their Shang Tsung is good (they're usually not), get right in there face and smash it.
- If you don't know Reptile well, take that guy into practice mode and figure out what he can and can't exploit. There are some really strong Reptile's out there, and if you don't know what he can do you're gonna have a hard time knowing how to punish him.

I use to play like that,but after i while i have got quite good at playing Quan chi .Now i pick him most times and win about 70% of my matches,Im ok with that. :3

Eh, I'd rather just pick a character I enjoy playing as. I'm not that competitive with the game, so if I get my ass kicked as Reptile just because this dude's Smoke is bounding all over the screen, then so be it.

I'd stay with a character you're good with and learn how to beat tough match-ups with that same character.

It's the only way to truly improve cause taking the easy way out will make you no better at the game.

By only playing sub-zero I've managed to work out winning strategies for almost every opponent (e.g. After knocking down an ermac, jump over him to dodge the wake-up and get a free opening) and I really feel it only comes down to skill when I lose and not tier lists :) .