I guess that is only because it was at first limited to Tallinn and even after the extension to all of Estonia you still have foreigners not covering the costs with their tax payments. I have no idea what fraction of the people would fall into the respective categories but I would guess that after the extension to the entire nation it is not really worth the effort and costs to make foreigners pay because they are a small fraction compared to the costs of maintaining a payment system.

Also, tourists tend to pay 'tourist tax' in one way or another so they're already covered to some extent.

The main question is who will really pay for a "free" service, which is obviously not free but rather is a kind of flat rate.

In the case of Estonia the expenses could be directly or indirectly covered from EU budget (which is filled by NL, DE etc.) and also the experiment is possible due to relatively low salaries. I cannot imagine such an experiment in NL.

There's no experiment and it has nothing to do with the EU. It's a local thing that didn't initially even have central goverment's backing. Public transport in Tallinn (1/3 of Estonia's population) was made free in 2013 and its expenses are covered from personal income tax from Tallinn's residents.

As to other towns and rural regions, which are poorer, the central government recently passed a measure to increase subsidies to municipalities in an amount that would allow them to make all public transport free, if they wanted. It's now up to municipalities to find a balance between fully subsidized, partially subsidized and commercial lines.

See my comment [0] for the reason why tracking is necessary for them.

[0] https://news.ycombinator.com/item?id=17108804

Thank you for that explanation, it makes perfect sense now.