I know I'm a nebie, but I feel like an oldbe having read this board for a long time, but never joined in! Sorry Fiona, at least I have now.
For me there are pros and cons to both.
With DIY, if you choose a scheduled flight you have that extra baggage allowance which is always handy, comfort - magic and a little more flexibility if you are able to take advantage of that. In Goa, you can stay at some of the lovely little guest houses or two or three, which I think are so much more cosy than the bigger hotels.
"Flight only" not so comfortable, but choose you own guest houses or two or three....
Flight and accomodation - no worries (usually). Everything is taken care of as long as you get to aeroplane! You know you have a base for the holiday which sometimes is a blessing.
For me, a big drawback (now) with the charter flights is the lack of luggage allowance :-(