I think that it would be proper to take a few things into
context when looking at Indo-Sing relations.
During Habibie's presidency, the first conflict occured when SM/MM
Lee mentioned in a interview that he believe along the lines that
Habibie would not last long. When Singapore offered aid to
Indonesia then, Teo Chee Hearn delivered the supplies to GEN
Wiranto, and not Habibie the president. To Habibie, it was a grave
insult, and it was following this that he uttered his little red
dot comments.
Looking at the current protests about 'toxic' waste, it seems to me
that the protesters hardly represented the Indonesian masses. Far
from Indonesians as a whole being ungrateful - it is far more
likely that the demonstrators were hired by specific interest
groups who wanted to sow discord.
How would the average Indonesian know about the contents of various
passing vessels? How would the average Indonesian know about the
Basel Convention? And the fact that the police was conspiciously
absent hints at the whole event being staged.
Given the precarious position of SBY now, it might be premature to
conclude that he was the one to sanction the event. Given
Singapore's various anti terrorism drives, including the provision
of evidence against the JI preacher Abu Bashir it is hardly
shocking that there are factions in Indonesia that have little love
for Singapore.