Why are you quoting political thinktanks as verbatim. Their job is to pick out facts and arrange them so that it suits their narrative. Let's shine some light on their spin:
(a) Japanese HSR. It started in 1964[1]. Is anyone surprised that it lost 50% of its market share to cars if cars were literally at the verge of becoming popular when it started? Japan is a huge car country. The relevant statistic here is that an average Japanese does 25x the rail kilometers per year an American is doing[2], yet has less car km per year[3]. They are second only to Switzerland in that statistic. Japan's railway companies are profitable, both as HSR[5] and local transport in big cities[4].
(b) Rail in Europe: Why are two countries picked out and then their success is measured by the market share in all of Europe, including the severely underdeveloped East? Europe is a big and diverse place too.
(c) "some environmentalist don't like it either" - I really don't see the relevance there.
The freight train system in the US is a good point - IMO Europe and Asia should take it as an example. I still don't see the relevance for passenger rail though, it's a separate issue. The question is: Does is make sense to push public transport, both locally and regionally. Given that (a) we have examples like Japan that clearly show how it can work and (b) environmental footprint of each person needs to be drastically lowered if we want to survive as a 6+ billion species, I'd put my money on 'yes'.
Edit: The USA is still the only big country with a carbon footprint way above 10 tonnes per capita and year. Americans still emit 1.8x the CO2 of Japan, even though Japanese houses have no isolation to speak of (earthquake safety / corrupt builders). It's getting better, but there's still a huge gap between the USA and and the rest of the highly industrialized world. Everyone needs to get better there, but there are a few countries that absolutely need to do a lot, or we're all fucked. So far I'd put USA, China and Russia on that list, soon probably India and Brazil as well.
[1] http://de.wikipedia.org/wiki/Shinkansen
[2] http://en.wikipedia.org/wiki/Rail_usage_statistics_by_countr...
[3] http://en.wikipedia.org/wiki/List_of_countries_by_traffic-re... (I don't have the source for car km per capita, but you can deduct it from this table)
[4] https://www.jtlu.org/index.php/jtlu/article/view/280/201
[5] http://www.jreast.co.jp/e/investor/financial/2013/pdf/2013_f...
[6] http://en.wikipedia.org/wiki/List_of_countries_by_carbon_dio...