Replacing antibiotics with proteins and possibly phage is a doomed proposition if done as a simple substitution. The advantage that antibiotics have that proteins can never match is they are low molecular weight chemicals. thus you don't have to give someone a high mass dose, it can be absorbed in the gut or membranes, and it can get into cells. Furthermore proteins are relatively easy to decompose without inventing any custom hardware, they are also easy to recognize specifically (which is also why they can provoke an immune response if not properly humanized). Thus proteins are not substitutes and start out with many many orders of magnitude handicap in molecular weight and accessibility. Therefore to overcome that one needs to exploit protein therapies in different ways. proteins are good at things like catalysis. The intital activity of a chemical is stochiometric in which one chemical binds one receptor. But an enzyme can turn over many many reactions, so one can, if used right, have a manyfold activity. (on the otherhand, this advanage is not clear cut, since the receptors bound by standard chemicals may amplify the signal as well, and many desired targets medical for proteins will be stochiometric binders not catalytic enzymes). A big big advantage of proteins is their potential for specificity which will both diminish their side effects and could concentrate them into a specific target area. Imagine for instance protein therapeutic which only affected a certain pathogen and left the other bacteria in your gut alone. Finally, if the protein is large enough then it can remain in the circulatory system longer before the body removes it. But that also means higher molecular weight which can be bad.
Phage are even higher molecular weight. But they can reproduce. And presumably they might be tailored to only infect the bad bacteria as their host for reproduction. But they also might become antigens and your own body would clear them.
Both of these therapies have killer applications and are not to be dismissed. Their extreme specificty will completely change medicine even more than antibiotics did. But they are not in the near future any sort of replacement for antibiotics.