Dash, my son will be 5 in a couple of weeks. I think the point is different children react differently - my three year old daughter had no problem with it all.
And indeed my son can watch other films which would think have more things in them that he might find scary but he is fine with them.
I think the reason was that he has really bought into Paddington as a character and did want to see him come to harm, where as with other more "cartoony" stuff that isn't the case.
The main point I was trying to make was that an adult isn't necessarily the best judge of what a small child might or might not find scary - the best judge of that is a small child, or really a group of small children.
I don't want to put you off taking your family to this as it is generally fine, it is just that boy did find it scary.