What might be the idea behind this?
First and foremost because they use different protocols.
FaceTime was created as an implementation of a new protocol for video calls. Apple has pledged to release this protocol/format in the future with hopes of other software vendors adopting it so there is opportunity for interoperability.
iChat uses a variety of protocols for chat interaction, most of which were originally designed to carry text as a payload. Video in most cases was something added to these protocols after the fact.
Consider iChat the 'legacy' way of handling video and FaceTime the new way.