Tony hates Bobby for several reasons:
even though he was the son of Johnny Boy Soprano had to gain experience by killing Willie Overall, and doing the robbery, during a game of cards;
1) Bobby is one of the few characters with Johnny Sack that does not have mistresses and deeply loves his wife;
2) Bobby has children who love him, while Anthony Jr. hates him, Meadowlooks at him from top to bottom and Carmela, is with him, just for the money;
3) Bobby became a soldier and then captain, very easily as Tony, but Tony the envy his happiness
Sorry if I quoted myself but I have also to say
Tony hate Bobby because:
1)Bobby thanks to his dad was made without haved killed nobody ( Tony must whack Willie Overall in 1982 and rob Feech La Manna;
2)Bobby loves his wife Karen and have a good relationship with the children that adore him (while meadow and AJ as well as Carmela are with him just for the money);
3)Junior respect Bobby and not his nephew;
4) Bobby was happy of what had,while the others (Paulie,Christopher,Tony ecc) are never happy of what they had;
5) Bobby don't have the vices that the other soldier had;
6) After Karen death,Bobby married Janice,and Tony hate his sister and every men that stay with her.
So Tony has begun to respect Bobby after he killed someone and beat him because so tony thinks, only those who are ready to kill and beat him, is a real man.
For me Bobby won't flip,also I would see him die with the AR-15 in the hands that whacked in a railway model store.
Everything I have written is my opinion, if I'm wrong, tell me where.
