What causes an atom to become positively charged?

First of all, atoms do not have to be positively charged. In fact, they are generally neutral. If you say you have an atom of say, Lithium, you can say that there are an equal amount of protons (positive charge) and electrons (negative charge) which leads the net charge to be 0 (there will also be neutrons in the nucleus, but they are neutral). However, if some electric field is present (just as example), there may be a loss of an electron which leads to increase in charge from 0 to 1 (you lose a - 1 charge nucleon).

To lose atoms that gain electrons to become positively charged