In the UK at least, decisions and rationale about which vaccinations and treatments should be publicly-funded via the NHS are published quite transparently. For example: https://www.nihr.ac.uk/story/preventing-cancer-extending-vaccination-boys

Vaccinating everyone in the UK against everything for which vaccines are available (even against diseases with very low risk in the UK) would cost so much that the NHS would have to cut treatments with very high benefit-to-cost ratio.

Therefore, below a certain benefit-to-cost threshold, the UK has no reasonable choice except to withhold public funding. The HPV vaccine for boys was right on that threshold. IMO, the UK did the right thing by funding the clear benefit (HPV vaccine for girls, whose risk was significantly higher per existing evidence) and extending it to boys when additional evidence showed it was worth doing so.

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Cost-benefit is the likely reason.

For comparison: the UK initially concluded the cost-benefit ratio was in favour of girls-only HPV vaccination, but IIUC updated this assessment and offered it to boys too after a public campaign by Jaime Winstone.