Personally I haven't seen negative reactions when I introduce myself as Pakistani. Most people are neutrally curious and just want to know about a place they have no idea about.
I am aware that Pakistan is projected in world media in negative light and so are Muslims. I would imagine there will be negative perception especially in western nations. Media is an effective tool to shape perception after all. However, Western citizens are not that much into world affairs, especially the Americans. They are more concerned about their jobs, entertainment and party life so there is that.
As far Indian citizens, they are amazingly ignorant about Pakistan. One of my friend went to India. He went to a shop to buy something. Through his fair skin (he is very fair and good looking. Please don't take it the wrong way) and accent, shopkeeper reckoned he is not a local. He asked where he is from, and answer resulted in everyone around to come to a stand still. My friend laughs so hard and tells how everyone inspected him from all sides for a minute or so before coming to conclusion he bears no resemblance to Pakistanis as they know from movies. They were expecting a bearded man with Ak-47 in his hand and here was a fair young man in front of them. Some were still convinced he is not from Pakistan. So perception of Indian citizens is highly influenced by media, politics and movies. I don't know if I should fault them for that. It is upto you guys.