Proliferate and Bloom Hulk
It gets only one +1/+1 counter. The creature has three +1/+1 counters, but each of those fall into the same kind of counter - the +1/+1 counter kind.

There are other counters. For example, Haphazard Bombardment places "aim counters". You could proliferate those too, although in this particular case it wouldn't have any practical effect. Other examples of counters are planeswalker loyalty counters, age counters (from cumulative upkeep cards), and so on.

MTG Gamepedia has a full list of all counters.