Mainly cost/benefit analysis. Using vaccines has a cost, both in dollars and in risk. That cost may be very low (cheap safe vaccines, like measles vaccine), or may be relatively high (smallpox vaccine is relatively risky, with around a 1 in 300,000 chance of moderate to severe side effects); but there is always *some* cost. 

Vaccines may not have any significant benefit. I live in the urban USA; it's unlikely that an Ebola vaccine would offer me any benefit (as of the current situation in 2019). Very few people in 2019 have a significant chance of being exposed to smallpox, since it's extinct in the wild; the benefit of universal smallpox vaccine would be small.

So if the risk of a vaccine is greater than the benefit, delivering the vaccine would be more harmful than good. This calculation is done as a routine, and the vaccines people receive are known to be ones that confer more benefit than risk.

In fact, with vaccines, the benefit needs to be *much* higher than the risk, because with vaccines the benefit is invisible (nothing happens - you don't die of measles) while the risk is something that happens. Typically, vaccine benefit/cost ratios are very high, for that reason.

Monetary cost is also a factor. It may seem harsh to think that saving a child's life with a vaccine is given a price, but at some point the finite supply of money can be used more effectively elsewhere. If it costs a billion dollars to give a particular vaccine, and it ends up saving one life, is that the best use of money? Could it be better spent on nutrition, sanitation, etc? 

This applies to quite a few diseases. There are, in academic labs and in the freezers of pharmaceutical companies, vaccines against a lot of pathogens that are not being used, because the cost is too great for the benefit. That's an equation that changes all the time; it applied to the Ebola vaccines at one point, but in the face of an Ebola outbreak those vaccines -- in those areas -- are now cost-effective. 

Finally, there are a handful of pathogens for which a reasonably-priced good vaccine would certainly be cost-effective (HIV, malaria, tuberculosis, for example) but for which reasonably-priced good vaccines don't exist, because vaccines are sometimes really hard to make.