They believed that audiences would stick around on iPlayer, and while Killing Eve and Class (both of which were marketed as BBC3 dramas) both got popular, no one was really going to stick around for content they can find elsewhere else
Two interesting examples here and they couldn't be more different. It's hard to argue Class was ever popular, the pilot I guess had some interest but I don't think it's in anyone but the most hardcore whovians consciousness - especially compared to BBC 3's first go at a proper Doctor Who spinoff in Torchwood. Then it was shoved out proper late night BBC one months later with pretty poor ratings.
If you look at Killing Eve, it was less BBC Three on One, more like BBC One with first look on Three via boxset. Would it have been as popular if it hadn't been going out primetime BBC One? Hard to say, I'd like to think so but it shows how much the lines have blurred since Three went online only.
That said, Killing Eve apart (which is an acquisition anyway) , what success has BBC Three had since moving online? Fleebag and This Country seem to be the standouts, but other popular shows such as Cuckoo and People Just Do Nothing were there on the linear channel. Maybe this will up the hit rate.