Hormonal contraception has been questioned since it's appearance on the market. It can increase blood pressure, affect cholesterol levels, increases your risk of some cancers, increase the risk of cardiovascular disease (especially if you smoke), and so on.
Then there are the moral issues. The obvious one is, "Is it wrong to prevent a pregnancy?" While there are some of us who may think that it is NOT WRONG to prevent a pregnancy, most of us would agree that it is definately WRONG to terminate a pregnancy. Doctors will not always tell you that the pill can actually lead to a spontaneous abortion, either because they are themselves not aware or simply because they do not think it should be a concern of theirs. As I understand it, the pill does NOT ALWAYS prevent ovulation, but the pill ALWAYS thins the lining of the uterus in order to make implantation of a fertilized egg (baby) almost impossible and therefore causes a spontaneous abortion. This takes place without the mother ever knowing that she is (was) pregnant.
Please take some time to read this study: http://archfami.ama-assn.org/cgi/reprint/9/2/126
If you do not have the time to read the article, I have copied and pasted it's conclusion here:
CONCLUSIONS
The available evidence supports the
hypothesis that when ovulation and
fertilization occur in women taking
OCs, postfertilization effects are
operative on occasion to prevent
clinically recognized pregnancy.
Physicians should understand and
respect the beliefs of patients who
consider human life to be present
and valuable from the moment of
fertilization. Since it would be difficult
to predict which patients might
object to being given an OC if they
were aware of possible postfertilization
effects, mentioning the potential
for postfertilization effects of
OCs to all patients and providing
detailed information about the
evidence to those who request it is
necessary for adequately informed
consent.