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As usual, I went outside the office to have a puff and as I neared the bird feeders, all the birds flew up into the trees. Now compare this with a scenario I witnessed in Chobe, Botswana. An Elephant came to drink and after drinking, just stood there with one of his hind legs lifted up. A dove came to sit on his foot as if it was the most natural thing to do. Now why was the dove not scared of such a big animal whilst the dove would have flown away if I was there.

And, why are some animals more scared of humans than others? You can walk past a Hadeda, and it will just sit and look at you, but a weaver will take to the air immediately.

Is it in their genes or DNA to be scared?

I think it is a nature thing.

because they have a good memories... of our bad "manners"

I have been feeding the garden birds for the past 12 years with fruit, leftover rice, bird seed, etc., and every time I go out to feed them, they all fly away. One would think they have become used to me by now, but no way! The only ones that don't fly away are the Crested Barbets.

@ Rooies: Even the Hadedas fly away when I go out! Then they sit on the roof, screaming at me!

I think this is true, perhaps they know or feel the dark side of human nature (as a collective) . But I think they loose some of their fear when they start to trust individuals.

I've heard that it is a primal fear of an apex predator.

Ive also heard they recognize us as a general predator due to our forward facing eyes.

I don't know what to believe.

Species evolution provides for behaviour that gives the best chance of an individual passing on genes to the next generation. To do that you first have to survive.
The dove and the elephant sharing a long history of co-existence have an understanding of each other's behaviour which allows for the interaction which Rooies described.
In places which saw no evolution/habitation of humans (like I think the Galapagos?), species evolved with no innate fear of homo sapiens.

What else can it be?

when I went to Ngorongoro, I was near a troup of Lions (6-8) and suddently all stood up... a group of Massaï with cattle went down the slope...
so there is a "connection" between human, the hunters we was, and animals need lot and lot of generations to forget... and it's better like that !
(hope you understand what I mean... english)

Does this imply that they will also be scared of monkeys and chimps?

Chimps can certainly be predators as can baboons, they eat meat when they can, although Gorillas do not. I am not sure how many of the other primate species are omnivores?

Whilst some apes eat meat I don't think they are anywhere near apex predator levels. Chacma baboons tend not to eat meat but as they are so adaptable they have been known to eat small mammals and the ones on the Cape Peninsula have adapted to eat shell fish!