So, yesterday when my doctor was going over my labs, he said my lab results show my hiv is resistant to protease inhibitors. They way he explained it, it sounded like some meds would not work for me. He did say that in that case I am a good candidate for a one pill once a day medication when the time comes. But don't these have protease inhibitors in them too?

No, the only regimen that is one pill once daily is Atripla, which contains the NNRTI efavirenz (Sustiva), tenofovir (Viread), and emtricitabine (Emtriva) all co-formulated into one pill.

I would suggest that you talk more to your doctor about the findings of the resistance test. It is unusual to have high level protease inhibitor at baseline, though as you suggest some patients will have one or more baseline protease inhibitor (PI) resistance that might reduce the effectiveness of one or more PIs. Your doctor can also perform an additional resistance test - a phenotype - that will assess your virus' likely response to all of the PIs, as well as to members of other classes.

It is common for two or three regimens during the life of a person living with HIV to include PIs, rather than only one regimen, so even though you have some PI resistance mutations, it is likely that you could still be treated at some point in future if necessary with a PI-containing regimen.