At *some* border crossings, why do bus passengers have to get off, but not those in cars?

When driving a private car, it is usually assumed that the baggage in that car belongs to the people in the car or was placed in the car by the occupants. And if any of the occupants warrant additional checks, the car is pulled aside for secondary inspection.

When riding on a bus, the baggage compartment is accessible to many people other than the occupants of the bus, hence it is easier for "extra" baggage to be loaded. By asking all passengers to claim their bags, you quickly find any "extra" items. You also pair passengers with their bags should anyone warrant secondary searches.

Ultimately you do the same when you fly, as you have to claim your bags after clearing immigration and before customs (with a few exceptions).

I have been asked to step out and formally identify my belongings before my car was searched at a land border so it does happen too.

Anecdotally, in trains, I have experienced very different treatments depending (apparently) on the class of travel. Profiling (based on appearance, type of car, etc.) does happen too in many places. So the treatment you get might depend on some (subjective or systematic) evaluation of the risk you present and/or the level of arbitrariness you can be subjected to without making trouble. And someone travelling by bus is unlikely to have powerful connections…

For example, in the cheapest class in a train, I once saw customs and police (three different agencies and six or seven agents in total) get on board early in the morning and spend half-an-hour asking loudly which bag belongs to whom, checking passports, phoning in to check mobile phone serial numbers against some database (yes, really). Travelling in a sleeper on another day, at the exact same border crossing, I handed my passport to the attendant in the evening and did not even have to wake up or open the door of my sleeper for the border check.

With collective means of transportation, another factor is that once you are out of the bus and waiting in line with your stuff, it's easy to pull you aside with minimal fuss and delay. Note that contraband is not the only thing police would be looking for, they also want to be able to filter people/prevent them from crossing the border illegally.

It would be more difficult if they would ask specific people to step out of the bus and identify their bags when it's already clear they have been been flagged for secondary inspection or worse. As @pnuts commented, people could also be tempted to “forget” their bag if something illegal has been found in it, which is not unsurmountable but would also cause delays.

Perhaps there is some profiling behind this. At a border crossing where, in the experience of border guards, trafficking (in the sense of not declaring taxable goods) takes places mostly by bus passengers, they will have a tendency to examine bus passengers more closely.

In order borders, specific car types or nationalities may be targeted. To take an example, expensive german-made cars going from Andorra to Spain are often targeted by spanish customs, since they often catch people with extra money on board (above the 9900€ limit).

In a train where some tariff classes are examined more closely than others, it may be a case of local people "border-hopping", buying more cheaply on one side of the border and then selling on the other. Naturally, these will acquire the cheapest seats on the train to maximize returns.