Forgive me for my ignorance, but why was Suharto targeting the ethnic Chinese? Were they grouped with the Communists?
Communism was a convenient excuse -- the real issues appear to be more class- and ethnically-based. There's a lot of backstory, including racial tensions and Indonesia's colonial history.
Wiki offers the following discussion on Chinese Indonesians. As always, there were a lot of reasons, not least of which was that the Chinese were fairly dominant in the Indonesian economy.