I'm sorry about your Father. My son is almost 4 (in March) and when he was 2 3/4 Grandpa Terry (my FIL) died, then GG (Great Grandma, my grandma) then after he turned 3, Granny (my MIL) died. And the cat...and the fish...and three great uncles (he didn't know them as well) - all within 6 months. So we've had some experience in a short time. Some died from cancer, some from complications from old age. He knows they are all angels in heaven and they're keeping him safe and loving him from heaven.
However, b/c so many people died in such a short period of time, he soon became concerned about death -- too much for a 2 or 3 year old. First we said they were sick and tried to explain cancer, but it was too complicated. Plus, he got very upset and frantic when I said Papa (my father) was sick (flu) b/c he thought Papa was going to die. Same thing when I got sick. So we didn't say "sick". Then we talked about them getting "old" but to him a lot of people are "old" and we didn't want him to think all his grandparents were about to drop dead (he was very worried about that too -- kept asking "Is Nonna (my mother) old? Is Buddy old? (the dog, yes, but he's not going to die yet)). So finally I landed on "exercize" as in "Granny died b/c she didn't exercize", which is partially true in a way. So when he asks if someone is going to die, I can point to my Dad and Mom "see, how Papa goes to the gym and skates with you? And Nonna does her exercizes with your? And Daddy and I go to the gym and play with you?" Even the dog and the baby exercize! The lack of exercize and movement made sense when the others died. This may not work for every family, but he seems to understand and accept this. I did try to explain that we're all going to die someday, but given all the death he's been exerience, it just made him so sad. A bit of truth, and a bit of redirection, given his age. And it make us have to keep exercizing too!
We did bring him to Granny's (his Grandmother) funeral. He was 3 and 2 months. It was at his church, he knew the priest, he knew Granny well and knew she was an angel. He did really well -- looked at her in the coffin and seemed to understand that her spirit was in heaven. We didn't take him to the burial (didn't want him to see her body actually going into the ground - too complicated to explain at the momment) but he has been to everyone's gravesite. I think it's important to still remember them, bring them flowers and talk about them.
Sorry this was so long! K.