On July 1st, 2008, Germany banned smoking in all 16 states, all across Germany. The heading of this article implies a nationwide smoking ban in Germany which is not the case. The bans are state laws, coming into effect between August 1, 2007, and July 1, 2008, depending on the individual states.
The authors mourn about a "bewildering patchwork of anti-smoking rules", a common slogan among German antis who do not very much appreciate the division of power inherent to a federal system. This notion itself is certainly bewildering to (among others) our American readers, for which a diversity of legislation between individual states is self-evident.
The article is misleading when it ascribes the "toughest public smoking ban" to Bavaria. Certainly, Bavaria is the only state which does not allow seperate smokers’ room in the hospitality sector, but no legal restriction is imposed on smoking in bars and restaurants for the time they are not accessible for the general public. This has lead to an enormous wave of "smokers’ club", i.e. members-only venues. The VEBWK (Association for the Preservation of the Bavarian Hospitality culture) raised 70.000 members and thousands of locations within 6 months. Combined with lots of individual clubs, up to one third or more of all hospitality venues, depending on the town or region, has become "smoking", or even better, "tolerant", because many non-smokers also carry the cards of smokers’ clubs when going out on the town.
Furthermore, the text mentions (provisional) judicial exemptions in several states for single-room bars with no employees. The authors forgot about one judgment (in the state of Schleswig-Holstein) expanding this relief to other bars as well.
From the linked article at least, the 3,300 "dead from passive smoking" (the precise body count is 3,301, of course), is referred to as a claim by an anti organization and not as the truth.
More about these aspects can be found in the Forces Germany English language blog which has an ongoing series of entries about the general situation in Germany regarding smoking bans.