Generally, newer bikes run tubeless tires. That said, there are a couple advantages to using tubes. First, it's easier to repair a tubed tire on the side of the road or trail. The tire slips off easier, and a tube with a small puncture is easy to patch or replace. Not so with a tubeless tire, which generally requires specialized equipment to get off the rim and repair. This makes tubed tires the choice of many recreational dirt bike riders -- when you get a flat in the middle of nowhere, you can pull over, fix it and keep riding.
However, there's a reason that most new tires are tubeless, and the reason is safety. Tubed tires are more likely to pop like a balloon in the case of a puncture. That's not saying tubeless tires won't burst or that all punctures of a tubed tire result in an uncontrolled crash, but tubes are more likely to pop than tubeless. Also, the comparatively looser fit of a tubed tire to the rim makes it a little more likely to separate from the rim in the case of fast action.
If you're running on tubed tires, make sure you keep the right pressure -- a floppy tube is a dangerous tube.