[NOTE: ProRes color handling has been improved with After Effects CS5. The following answer is for After Effects CS4.]
See these two articles about how to interpret ProRes media by assigning the correct input color profile and by making sure that the appropriate QuickTime gamma tag is applied on ouput.
In After Effects CS5, we fixed some bugs for ProRes 422 and ProRes 4444. But we still have a couple of issues.
This post gives workarounds for two issues in After Effects CS5: "ProRes 4444 and ProRes 422 in After Effects CS5"