Trademarks are an interesting study in Law. Large companies such as airlines can usually protect their brand from other similar marks, but not always. Especially when the trademarks are in two entirely different industries. For instance, if there was an airline named Apple, the computer company may have no ability to stop it because there would be little confusion to consumers over what product/service the two companies are offering, they are very different.
In this case however, you could argue that both JAL and the Czech trucking company are in the transportation and freight business, which could certainly raise concerns.
I suspect that in this case however, it comes down to the specifics of Czech copyright law. In a more famous case, Budweiser (the beer brand of Anheuser-Busch InBev) is not permitted to use it's brand name in the Czech Republic due to a local Czech brand of Bud that existed before the American beer arrived there. Despite years of legal battles, A-B was never able to win in Czech court.
Not to mention, JAL does not do business in the Czech Republic, so it probably has very little ability to defend it's brand there.