Lets forget about the fact that Jirayja would indeed easily be amaterasu'd theres no argue about that
urm no, tobi saw the eyes bleed and everything, he simply COULD not react in time
You have to realize that it's reaction time + hand seals to make up the full time of this process.
what you're going off is if he had instant reaction time, which is impossible.. maybe minato and raikage A could pull that off .. but normal ninja? no.. not even tobi could do that
The situation tobi was in : he was shocked and didnt have his guard up i think thats why he took a clean hit from amaterasu , i really doubt in an actual battle he would get hit with it
When fighting he could react to it
the situation in the cave he couldnt ever have known that sasuke suddenly would just use amaterasu like that