I presume we are talking new beetle here? Ive got one, well my wife does at least. It's 4 years old now, never had a problem with it leaking at all. It is a pretty solid soft top, 3 layers I think, insulated.
The windows drop 1cm or so when you open the door and then seal up onto the roof when you close them which gives a very good seal, if that makes sense.
I tend to make sure I look after the soft top though, clean and re-proof it every couple of months just to be safe.
Getting bikes in it or on the back of it though, that is a whole other problem.
I also know a couple of people with soft top minis, both of which leak, but that may well be bad luck.