I'd wager that most of the people you see bagging on PayPal have:
1) Never used them in a business capacity
2) Have only read horror stories
3) Take those stories at face value
The horror stories usually have an obvious, "duh" kind of reasoning behind them when you step back and think about it from PayPal's point of view. Big influx of sales out of nowhere? That's a flagging. Accepting money for some kind of charity? That's a flagging.
I'm very satisfied with their service. They work to protect your money, your customers' money, and their reputation. If you're an entrepreneur and you aren't sure what payment processor to go with, don't exclude PayPal from consideration.