No matter what people say, Nepal is opressed by India politically, economically and in many other ways and the way they potray Nepali in India (as Gorkha, not the way British potray us as brave soldiers but as paale, chaukidaar, nokkar) breeds the hatred furthermore. These are some of the reasons.
Just because another country is strong does not mean that they have to be worshipped. Just visit UK and you will see how much Americans are hated here, though the hate might have subsided since Obama got elected. Also go to France and see how much British are hated there and even within UK, Sottish hate English and treat them as enemy in support for European counterparts. When there is a community the powerful ones are normally hated by the ones who are marginalised.