It could be the Titans were an older set of deities whose worship was supplanted by the Olympians - hence the Titan War - and they were cast as malevolent by Olympian priests to make their cults increasingly unpopular. And perhaps this view has just persisted to modern times because nobody thought to change it.
There's another possibility - I'm reading a book on Dionysus just now which mentions the Orphic Mysteries It quotes Pausanias who lived in 200CE, author of Description of Greece describing the creator of the Orphic Mysteries, a man called Onomakritos thus:
"in the orgies he composed for Dionysos he made the Titans the authors of the god's sufferings".
It could be that minor innocuous changes to local myths and cult practises here and there (like the one described above) led to the Titans falling out of favour with the Hellenes.