He went back to kill Barry as a baby.
20somethign year old Barry could destroy his time machine? or more accurately, if Gideon is his time machine, Barry broke her.
Besides, the newspaper talking about dinosaurs at the zoo was translated as being holes in time created by the Crisis.
It is very possible that Thawne is trying to kill Barry because he thinks that doing so will prevent the impending Crisis.
At this point, it looks like we might have a Flashpoint universe storyline set up. Hopefully that would be something that could last a few episodes.