First, from the legal point of view, the principles of "interdiction" as the main provision of the PSI are in contradiction with the 1982 UN Law of the Sea Convention. There is nothing in the provisions of the convention that would allow a country to intercept a vessel in international waters on suspicion that it is carrying weapons of mass destruction.In other words, US bad. Even if the goal is to curb terrorism and keep the sea lanes open.
While suspicions about such vessels or ships will be based on intelligence information, we should bear in mind the controversy over the legitimacy of intelligence information provided by the U.S. and the UK in the case of WMD in Iraq.
Furthermore, the nuclear-weapon-states such as the U.S., the UK and France have continuously worked to ensure that their ability to transit weapons of mass destruction is not hampered by nuclear-weapon-free-zones in some regions. They also have asserted their rights to transit nuclear materials through the high seas and through the EEZ's of coastal states, including Indonesia. It is also apparent, for the sake of commercial purposes, some major supplier countries do export sensitive WMD materials and technology upon the high seas and territorial waters of states.
Second, from the political point of view, the process of formulating the PSI was selective, unilateral in nature and not multilaterally negotiated. The goal of this Initiative through interdiction is pre-emptive and originally targeting only the "proliferators" of the "Axis of Evil" states.
... Many Asian countries remain reluctant to be openly associated with a U.S.- sponsored program like the PSI, either because they fear it may override national sovereignty and freedom of navigation, or they do not want to be tagged as a follower of the U.S.
Finally, it is a matter of principle that international law cannot maintain its integrity if applied discriminately, or if defined only by a "coalition of willing states". If members of the international community begin to allow the erosion of the UN Law of the Sea Convention, they should not expect that such concessions would be easily reversed.
UPDATE: Corrected title per comment by Alex.