The reason for six religions seems to be related to Indonesian blasphemy laws, in particular the 1965 Presidential Decree of Blasphemy and the later clarification which named those six religions as the religions of Indonesia.
1965 Presidential Decree of Blasphemy: I could not find the original full text of this decree, however it seems to be cited in multiple places and this site offers a paper containing excepts from it. Assuming that these excerpts are genuine, the following is the first article of the decree:
Every person is forbidden to intentionally tell, suggest or ask for supports in public to interpret the teachings of the religions, which exist in Indonesia or to perform religious practices similar to those religions, which deviate the mainstream teachings and practices of the religions.
Though this translation seems a bit odd, you can see the underlying source of why certain religions are recognized. In particular, "religions, which exist in Indonesia" are the only valid religions, and practicing similar religions but "which deviate the mainstream teachings and practices of the religions" is not allowed.
Why those six: According to the linked paper above, the 1965 decree was later clarified. I could not find the clarification(the paper has a poorly written bibiliography), however the paper claims the following:
...the phrase “religions which exist in Indonesia” refers to Islam, Christianity, Catholicism, Hinduism, Buddhism, and Confucius. It further explains that “the admission of these six religions can be proven by the history of religions in Indonesia because they are followed by most of the citizens throughout Indonesian archipelago. Therefore, the decree 1965 is applicable for these religions. However, it does not mean that the other religions, such as Judaism, Shinto, and Taoism are not allowed to exist in Indonesia.
(In the above, 'Christianity' seems to be synonymous with 'Protestantism')
Essentially, the reason those six religions are the officially recognized religions is due to the fact that, in 1965 at least, those religions represented the majority of Indonesians. Others religions, that aren't considered 'blasphemy', were simply not considered large at the time nor a part of the "history of religions in Indonesia".
Why not more: There are laws against publicly expressing hatred of or disgracing the main religions in Indonesia, and this apparently is taken to also include 'deviations' from the main religions. This likely makes expanding the list of officially recognized religions difficult, as more religions would require expanded interpretation of what 'deviations' from the religions actually include. As of right now, it seems like blasphemy laws do not cover 'unofficial' religions like Judaism or Orthodox, and adding these religions would likely cause conflict.