One of the reasons given online is that when Taiwan (then Formosa) was ceded to Japan in 1895 during the Qing dynasty, the Taiwanese thought it a lateral move -- one set of oppressors to another.

Japan embarked on several public works projects during its colonial rule, aiming to make Taiwan a showcase colony. Formosans were then placated only to adopt a wait-and-see attitude.

Still doesn't explain pro-Japanese sentiment.

Taiwanese say it was because Japan was not as brutal as its Qing predecessors.