On one hand, it is next to impossible to physically check 100% of cargo, especially when considering the timeframe. By allowing the shippers to take part in security procedures, the need to check every container goes down.
On the other hand, legitimate companies that play by the rules and have a low-risk security profile can be suborned by a number of methods (blackmail, corruption, extortion) into shipping threat materials into the United States.
I think that the benefits of C-TPAT outweigh the risks, but I understand there is a significant risk to the process.
I seem to remember some discussion of the problems of drug smuggling via container prior to 9/11. After 9/11 C-TPAT was the best option for security for the vast amount of cargo to check; it is still etter than nothing, but a "suitcase nuke" could still be walked across the border even if C-TPAT was at 100%.
Our best solution is to attack the terror ideology at it's sources, and be preemptive in that regard. But we should still maintain customs and border security measures as best as we can do.