Despite all of the wonderful advantages associated with BS/MD programs, they are not appropriate for all students. There are several potential disadvantages.
Most of the BS/MD programs prohibit a student from applying to medical schools other than the one associated with the program. While this may not seem like much of a disadvantage, medical schools have personalities just like colleges. What is an appropriate medical school for one student may not be the most appropriate for another student. By committing to a particular medical school early, you may be sacrificing the option to attend another medical school that may be more appropriate.
A second disadvantage may exist for those programs that are shorter than the traditional four years of college. If you decide at some point during college that medicine is not what you wish to follow as a profession, there can be problems associated with graduation requirements.
However, the biggest potential disadvantage is a practical one. If you are academically competitive for BS/MD programs, you are likely to be a strong candidate for medical school even if you follow the traditional route of four years of college followed by application to medical school.
Many of the BS/MD programs exist at colleges that may be weaker academically than you would traditionally consider. If you decide to follow a traditional path to medical school, you will likely attend a more academically competitive college. By attending a more academically competitive college, you will often be a stronger candidate for a more competitive medical school.
By going to a more competitive medical school, you may be in a better position to get the residency program you desire. The BS/MD programs limit your options. Whether that disadvantage outweighs the numerous advantages is for you to evaluate.
This potential disadvantage assumes that you maintain very high grades and very high MCAT scores and unfortunately, that is not always the case, even for very bright students. I have often seen students who have gone the traditional route but made a mistake in the major they chose or struggled with the MCAT. Some of these issues can be addressed by the lower GPA and test score requirements of BS/MD programs.
Only you can say whether a BS/MD program is right for you. And to answer that you need to understand the advantages and disadvantages.