I decided to do the cheap way and hitch hiked to Rurrenabaque from La Paz. It was real fun, though i must say it was also very dangerous. It took us a bus ride to the first village outside la paz, then we stopped the first truck on our way to rurrenabaque with my friend. you can read the full story on my blog http://galjanos1984.wordpress.com/2010/03/24/breaking-the-death-road/
If your destiny is Rurrenabaque, prefer the air transport way. Roads are extremely dangerous and mismaintained.
The best and comfortable way to explore this wild place is by motorboat excursions and complemmentary hiking expeditions.