My CPU is a AMD Phenom II X4 945 3.0 GHz and my GPU is a GTX 560 Ti. Is there a bottleneck? I notice people with the same GPU are getting a lot higher FPS then me..
Not really a bottle neck but depending on the game you will notice that Intel Core i5 and i7 CPU's can really help with frame rates. Not sure why but just a fact... And for that reason gamers usually prefer Intel Core i5 or i7 CPU's when making a build these days.
Personally I have an AMD Phenom II x4 955. It's fine for budget gaming as I was unwilling to pay Intels high prices but I guess that means I don't get the frame rate bonus that they seem to offer. Also, that frame rate bonus I just referred to depends on the game. Some games the difference is't so noticeable.
You should check to ensure that you DON'T have driver graphical enhancements turned on. Don't have AA and other effects that can be enabled in the driver turned on. Instead set it so it's managed by the game, then just use the settings/enhancements within the game by setting it to the desired graphics level. Disabling these enhancements can allow for a higher frame rate at the same graphics settings level.
Lastly, do you know if those people have overclocked their GPU's? If that is the case then yeah, they are going to be faster.
I would run something like Heaven benchmark to isolate your GPU. Heaven doesn't care about CPU at all, really. I've tested it with two different CPUs (Pentium G2020 dual core @ 2.9 vs Core i5 3570K @ 4.5GHz) with a GTX 670 and there was absolutely no difference in the score.