Flea has recorded with a few different filters including the Bassballs, Boss Autowah, FX25 and a MuTron III with dying batteries (that's on Sir Psycho Sexy) and for quite a few years he's used a Qtron when playing live.
The example I use for his FX25 sound is the break of "Power of Equality" off Blood Sugar Sex Magik. You can hear it at the 1:58 mark here:
Red Hot Chili Peppers - The Power Of Equality - YouTube
Scrappersa has it right that he's playing hard. He's slapping with a pretty aggressive attack to boot. And in this case using a pretty hot bass (a Wal).
I'd try setting the frequency of the DOD at around 1 o'clock and then adjust the Sensitivity until you get the filter to open the way you want based on your bass and playing style.
Good luck.
Oh, and just because I think it's worth noting that Flea doesn't seem to have many hangups about gear, you can hear the same break live where he's using his Modulus and (what sounds to be) a Qtron.
The break is around 2:30
Red Hot Chili Peppers - The Power Of Equality - YouTube
Sure, the filter sound is very different if you're really listening but it still sounds like the recorded version. Point being that technique/attack plays a huge role. For people chasing a particular tone of course the gear plays a huge role, but don't forget how much the hands always factor into things.
