Patriotism in itself is neither good nor bad; the problem with it is about how easily it can be exploited and turned into aggressive jingoism, arrogance and xenophobia. It can also be exploited in order to distract from domestic problems. The attention span is limited; a nation that's bathing in jingoism might forget about its solvable problems. It might even be stupid enough to overextend its resources because of jingoism fantasies.
That being said, outbursts of patriotism or nationalism (or even jingoism) have been very rare to non-existent in Germany during the Cold War (both East and West).
The 1989-1991 period (reunification) saw a revival of the "nation" idea. The old generation was fully aware that Germany was a divided nation, but for many of the young generation the German states were already different countries (similar to Germany and Austria today, but shh! - don't tell Austrians I wrote this!).
The football world championship 2006 hosted by Germany was IIRC the tournament that brought the breakthrough. Suddenly, we had all those German flags on cars, hanging outside windows - black-red-gold decoration everywhere. Almost like Christmas, only different colours and more. That was a very uncommon sight, but the later football championships (European and World) saw repetitions of the pattern, and it has become a custom. We're patriots in public for a couple weeks every 2nd year now.
The European Football Championship 2012 in June will show this again.
Don't be scared if you see lots of German flags. We don't have enough tanks these days to ruin your lawn. Everything is fine. ;)