The first subatomic particle discovered by scientists was the negatively charged electron. Why did scientists conclude that the atom also contained positively charged particles?
It had long been known that the atom was electrically neutral. Thus, if one part was negative, some other aspect had to carry positive charge.
In fact, Thomson's first "guess" was that the bulk of the atom was a positively-charged ball of fluid-like matter, with just enough positive charge to cancel the negative charge on the electrons that he envisioned as being stuck into the fluid "like raisins in a pudding".
The awareness of positive particles within the atoms came about ten years later, thanks the Rutherford's famous alpha-particle experiment.