Zacs - I understand the charter flights don't operate to goa during the rain season as the majority of people travelling do so as tourists and visitor numbers are hugely reduced at this time.
From Wikipedia:
"Several European charter airlines fly to Goa seasonally, typically between November and May. Flights from the UK (London Gatwick & Manchester Airport) are operated by Monarch Airlines, Thomson Airways & Thomas Cook Airlines."
Zacs they only fly approx. Nov to beginning of April, after that all the tourist stuff packs in and its like ghost town everywhere as most of the shops etc are closed, restaurants close and their workers who have migrated in for the tourist season return back to their homelands.
if you want to visit after that you have to fly schedule & change planes in Mumbai.