Did you get this from Wikipedia? If you did, I sympathize; all the entries related to this give no explanation for the phenomenon. If you didn't go there . . . Well, it won't answer your question.
But I think I've found the answer somewhere else. I'll go over some background stuff for anyone out there who doesn't know much about this, to make it a bit clearer (although you should be able to skip all this). Protostars are small pre-pre-main-sequence objects. At first, they aren't more than small clumps of gas and dust in a stellar nursery (a special nebula, perhaps). Soon, though, more matter begins to come towards a clump, and gradually the clump builds up enough matter that it begins a slight gravitational collapse into a definite object. Temperatures build, and eventually the object becomes a pre-main-sequence star.
These pre-main-sequence stars begin to accrete matter (here's where you should stop dozing off) into a circumstellar disk. At the moment, it doesn't matter if the disk will become a protoplanetary disk or something completely different; for now, we can treat it as a circumstellar accretion disk. Matter "falls" into the disk and towards the star; the star absorbs most of it. However, something else comes into play, and that's the star's magnetic field.
A lot of objects in the universe have magnetic fields, and a young pre-main-sequence star is no exception. It's field may be stronger than that of the Earth - so strong, in fact, that some of the matter in the circumstellar accretion disk follows slightly different paths than it normally would - paths along the field lines of the star's magnetic field. While there isn't enough evidence (scarcely any at all, really) to support or, more importantly, disprove this idea, it is though that the magnetic field lines lead the matter towards a point on the star, perhaps at its poles, and then compress it together into an astrophysical jet (or bipolar outflow) that shoots out into space. Such jets are often associated with other cool phenomena, such as Herbig-Haro objects.
So for everyone who considers this post a "Too long; didn't read" answer, here's a summary:
The truth is that nobody really knows. The current explanations for this phenomenon are that they are caused by matter from accretion disks being concentrated by magnetic field lines onto a single (well, double, one on either end of an axis) point, which then becomes an astrophysical jet.
I hope this helps.
Note: This paper, specifically the second page, was extremely helpful. Other pages that might interest you (or provide more information for those who are curious about this and related topics) are:
Herbig Ae/Be star