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It's probably just a matter of personal preference for what I would like on the flag. Putting the aboriginal flag onto the national flag is separating our pre-colonial history - on it's separate part on the flag.I think that the culture that has existed here for tens of thousands of years should be recognised as a part of the flag; the flag would represent us as a whole with that small part simply recognising that Australia existed long before 1788.
I'm not sure why you feel like we have to separate our pre-colonial history and set it aside as something 'other' as if it has nothing to do with the nation we are now.
A can abide people who specifically want that on the flag - I get that point of view and I don't think it is "wrong". But it is a kind of separation, a selection of part of (and arguably the most deserving such part by the way) Australia to get its own special place on the flag. I'd prefer a flag that has a broader remit. I guess the downside of trying to include everyone equally in that sense is that you might end up with something somewhat meaningless. But does that matter? Canada's maple leaf isn't all that significant or profound but it looks nice and is definitely Canadian.