If you read the actual study, the patients that actually took the medication as directed (didn't skip doses) and used condoms, decreased their risk by 99%. The 44% included "intent to treat" which means all the patients who signed up but didn't take the medications because they forgot, dropped out because of medication side effects, took medications intermittently, didn't use condoms, etc.

As for the disclaimer for IV drug abusers and M-F sex, since they have active studies looking at these groups, they can't comment on whether this drug is effective in these groups. Obviously gay males will be at higher risk than M-F patients with partners infected with HIV, but the risk of side effects for the drug itself makes the question different. IV drug abusers have a different infection model that doesn't apply to this study, and it would be irresponsible to assume that the results would be the same.