Why is Doxy-PEP less effective against gonorrhea?

It's a matter of resistance. Over the years, many strains of the gonorrhea bacterium have evolved and become resistant to doxycycline. As a result, the drug is no longer as effective at eliminating the infection. That’s why Doxy-PEP remains an excellent tool for syphilis and chlamydia, but offers only partial protection against gonorrhea.