Because if you tell people that condoms won't protect them from everything or protect them all the time, then people won't use them.  It is hard enough getting people to use them when they believe they could get a life-threatening disease without that protection.  So, imagine how many more cases of AIDS, and all the other STD's would occur if people didn't use them at all.  Condoms keep the levels in check.  And, they do prevent many people from getting these diseases.  Not all, but many.  Doctors have an obligation to protect their patients.  And, since abstinence is the only way to prevent STD's, and we all know that very few people will forgo sex indefinitely, physicians are doing the responsible thing

I do think that they should explain that you can get herpes in your mouth and HPV in your anus and throat.  Not enough people use condoms for oral sex.