As a programmer I'm more inclined to dislike things like the Game Factory, etc. that make it waaaaay too easy to make bad games, but I will always appreciate the effort that is put in to making a truly enjoyable, unique game, no matter who or what made it.
However, I will respect an author far more if he programmed a game himself.
In the end, a good game programmed entirely from scratch using no "game builders" will always be better than anything made using a "game builder". The easier the game development process becomes, the more similar and repetitive games will become, until there is only a vague sense of originality left. The fewer creative restrictions you have, such as those that generally accompany "game builders" , the better the end result will be.
And some of this applies to Flash vs. C++/Java/whatever--some restrictions had to be applied to make the development process easier. I'm sure if we all spent the time to make games in other, less restrictive languages, we would be much happier with our work.