Because Switzerland and the Czech Republic are both in the Schengen area, you may visit Switzerland using your residence permit (in connection with a valid passport). Strictly speaking, you are limited to spending no more than 90 days in any 180/day period in Schengen countries other than the Czech Republic, so if you have just spent 90 days in Slovakia, for example, you should not travel to Switzerland. However, this rule is not systematically enforced, so for casual travel around the Schengen area you don't need to worry too much about it.
Whether you are allowed to enter Switzerland does not depend on how you travel there. However, the likelihood that you will encounter immigration officials checking your passport and residence permit is probably different in the different modes of transportation. If you encounter such officials, however, you can just show your passport and Czech residence permit, and that should be the end of it. They might ask you some questions about the nature of your trip, but as long as those questions uncover nothing to arouse suspicion, they should allow you to enter Switzerland.
Since you've asked here on Expatriates, I would add that you may not move your place of residence to Switzerland nor accept employment there on the basis of a Czech residence permit or work permit.