Bitcoin transactions aren't completely safe, etc - they can be traced and whatnot. However, they are a lot more secure than payments through things such as PayPal, for example, and to the average user, Bitcoin is pretty much anonymous.

As for how it can be used harmfully - unfortunately that's how things just work out with this type of technology - to fund something in full secemret or whatever. Things are being done to stop illegal activity and Bitcoin, with an example being laws being passed in Australia to make it harder for things such as money laundering to happen with Bitcoin (don't remember the specifics, a quick google search away).

In the end, it's inevitable that tech such as Bitcoin is going to be used for bad, and it's best we just accept it.