Ach, we have no real issue with the accent. It's just often the first warning sign that you're speaking to a twat.
I know plenty of cool English people, some are even friends and family, but I also know plenty of twats. Every country has twats, but England seems to have them at a higher rate than many others. So Scots may be wary if they hear an English accent because of a disproportionately high amount of twats, but as long as you're not a twat then all's good.