Organic chemistry logic is in a way different from the logic taught in general chemistry classes, so when you are exposed to the organic chemistry - even if you have general chemistry behind - it seems completely alien. As GenChem101 comes always before Org101 almost every chemist have seen that problem, hence many people think organic chemistry is difficult. It is not, it is just in a way different.
In my case, reactions start off not neing too hard. You have categories to help you figure them out (addition, elimination, substitution, condensation, hydrolysis etc...), and you learn what to look for. Working with larger molecules is tough, because you often have several reactive groups and possible products, and the molecules react with themselves, which I found to be the most annoying part. This is at least the case on a third year high-school level.