You asked a fair question, and were not snide about it as many of the similar postings on this forum so I'll give you a legitimate answer.
We're patriotic, those of us who are anyways, for the very reasons you stated. We've been born to, or immigrated to as the case may be a magnificent county full of natural beauty. The generations that came before us took 13 obscure British Colonies and built the mightiest and most prosperous nation on the planet. We're impressed by their accomplishments and want to celebrate them so that we might emulate them and carry their legacy forward.
As to to the flag, it is a symbol of particular cultural significance to people of this country. When people disrespect it, they feel the country they love and the legacy they are proud of is being disrespected. Now, after scanning the article you linked I agree that some people are jumping to conclusions with Kaley Cuoco, as it appears it was a. not her and b. not meant as disrespect. It is easy to understand though why they might have come to that conclusion with deuchbags like Colin Kaepernick going out of their way to disrespect the flag, the anthem, and the country.