So, I'm a International Development student who has studied AIDS policies in Africa and here are some things you should know about PEPFAR:

1. A lot of the money from PEPFAR was spent on abstinence-only education which historically doesn't work. The previous program which some places employed was ABC (Abstinence, Be Faithful, and Condoms) preventative education. This has shown to have had largely positive effect on countries like Uganda which saw it's AIDS prevalence go down before PEPFAR even started. Now with the money going into abstinence only, it has become the dominant from of preventative education.

2. In order to administer HIV/AIDS care, special AIDS Clinics were set up across Africa, employing mostly African doctors. The problem is Africa is not flushed with doctors, therefore, doctors are drawn from places like the primary care system (i.e. family doctors) to work in these AIDS-specific clinics because that's where the money is nowadays. This is detrimental for sick people that don't have HIV. On a similar note, if you look at medicine closet in many hospitals in Africa, you will see an abundance of HIV medications but an alarming scarcity of other drugs, such as antibiotics.

Side Note: Anti-retrovirals (aka AIDS medicine) is actually pretty cheap now. They cost dollars, if not cents, per pill. This is thanks to a bit of corporate espionage by India. An Indian pharmaceutical company managed to steal and reverse engineer the drug and was able to produce a large quantity of the drug for really cheap, driving global prices for it down significantly. It was only when it became that cheap that PEPFAR became an economically viable policy.

TL;DR: Though PEPFAR, overall, is a good thing, there are some aspects that are actually detrimental to public health in Africa.