I am not saying that the scarecrow is NEVER a threat, but Batman makes routine busts of criminals, including supervillains, all the time. Scarecrow is sometimes one of them.
Not to mention that in the context of the movies he wasn't anywhere near the level of the Joker as a threat. Scarecrow is pretty much a one-trick pony with that fear gas, and though he may disperse it in creative ways, it is pretty much expected that that is what he is going to do. So, RELATIVELY the Scarecrow is a minor threat in comparison to some of the other rogues in the gallery.
Regardless of the threat the Scarecrow poses, it isn't out of the question for Batman to bust him quickly and I am happy they used him for continuity rather than having Batman bust some random criminal.