“在公交车上”到底是in the bus还是on the bus？

我在公交车里吃午饭

可以说成

I ll have lunch  in  the bus吗?

有人说 on  the bus这个搭配更常见

但是 on  the bus

总给我一种在车顶上的感觉

到底应该怎么理解呢？

The phrase  on the bus  is quite standard and normal. 

on the bus这个短语是一个很标准很普遍使用的搭配。

The use of  on  does NOT imply that the person is on the roof. Basically, if the speaker is taking a long trip by bus, that person is said to be  on the bus  during the entire trip. 

这里on的使用，并不是意味着这个人在位置层面的on。基本上，如果一个人说他搭公交车旅行，那么就应该表达成他在旅行中一直是 on the bus 的。

When a person is boarding a bus, we d typically say the person is getting  on  a bus. (And at the end of the trip, it would also be quite normal to say that person is getting  off  the bus.)

当一个人要搭乘公交车，我们就会说这个人正在get  on  a bus。（并且，当他下车时，我们会用get  off  the bus来表达）

究竟什么时候用on什么时候用in？

If there is no compartment involved, you get ON it. (bicycle, motorcycle, skateboard, etc.) (Note: partial compartments, such as those of convertible cars or open-topped boats, count as compartments; pretty much anything where the vehicle at least partially surrounds you.)

如果交通工具没有隔间，你就用on。(自行车、摩托车、滑板等)(注:有不是完整隔间的，如敞篷车、敞篷艇等，也算作隔间；几乎就是有东西遮挡在你周围就算是了。)

Oddly enough, if the transportation is large enough to allow you to move around freely, you also get ON it. (Bus, train, large boat, passenger plane, etc; anything with an aisle or walkway.)

尽管很奇怪，如果交通工具大到可以让你自由移动，你也用on。（公共汽车、火车、大型船舶、客机等;任何有过道或走道的东西。)

Otherwise, you almost certainly get IN it. (Car, personal aircraft, canoe, etc.)