While Borobodur is many things, it is not Hindu. The friezes on the site are stories from the life of the Buddha (and his past lives) and the monument itself is capped by a large number of Buddhist stupas.
Technically, the term "Hindu" as defined by the British just meant non-Muslim. In fact, it was the British who popularized the term Hindu in the first place since prior to British influence, there was no such religion, just a broad set of different religions such as Shivaism, Buddhism, Vishnuism and numerous others. In many places such as Assam, Buddha is revered by people who are labeled as Hindu.