True Nepali, more often than not, the primary intent of usage of the term "jyapu" is to ridicule/abuse someone belonging to Newar community. One could say the same about "bhote". Whilst the term in itself isn't derogatory, the implication makes it a word that tends to offend others. 

Nepalese in general can relate to this, too. How many of us take an offense when mistaken for a Indian, a middle eastern and in 'worst' cases, a Mehican?