most common cause of irregular periods is PolyCystic Ovarian Syndrome. There is a pretty exhaustive FAQ on it at INCIID.org: http://www.inciid.org/faq.php?cat=infertility101&id=2
As for why GYNs are so fond of blindly prescribing BCP to "treat" it, JenniferH is right on. It's a matter of not knowing enough about it. Which is kind of sad, as PCOS is also
the most common cause of infertility among women of childbearing age.
I know TCOYF covers PCOS in some capacity, but I'm not positive how much offhand. I'd have to uncover my book to answer the question, and as it's almost 1AM here right now, I'm not quite awake enough to do that. (Yes, I know that begs the question of why on Earth I am awake right now.)
Irregular periods of any cause absolutely will impact fertilty. It makes it that much more difficult to determine when a woman ovulates, especially if she's merely counting, or expecting ovulation to magically occur on day 14, as so many women seem to. PCOS can make things even more difficult, as it means that cycles are quite likely to be anovulatory (no egg released), and it screws around with your CM too for a lot of women...and over the counter ovulation predictor kits aren't accurate for women with this condition, as there can be an LH surge, or the appearance of one, without actual ovulation. One of the hallmarks of PCOS is that the first part of the cycle is perfectly fine, but where a normal woman would release an egg from the matured follicle, a woman with PCOS will have something go wrong at that step, and wind up with nothing at all or a cyst instead of a released egg.
There are many pharmaceutical treatments for PCOS, but a woman may well have to be quite persistent in trying to get proper care. For all that this is a common syndrome, it is my experience that it is also quite often misunderstood, esp. by doctors. I had one, in fact, tell me that I had PCOS because
I was overweight, when in reality overweight is the symptom rather than the cause. It can also be treated with homeopathics and with diet. (If I am not vigilant about avoiding refined sugars & flours and such, my symptoms come rushing back strongly.)
It is something well worth learning about, being connected as it is to both Type-II diabetes and also a long-term increased risk of heart disease.