Thanks Hugh
Some thoughts on this (having read the Directive)
http://europa.eu.int/eur-lex/pri/en/oj/dat/200 4/l_166/l_16620040430en01240143.pdf
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This directive intends to streamline toll charges across the EU to avoid congestion at toll plazas (from exerience, a bain in the life of Irish motorists). It does not state anywhere that all roads must be tolled, instead referring specifically to increasing ease of use on roads already subject to tolls. Where non-electronic tolling is in operation, electronic versions should be introduced and this will be the same system across the Union, so that drivers from other countries still pay to use roads when they travel to other member states.
Therefore, if your govt is quoting this at you as a reason to tax you off the road, they're lying to you. However, I doubt you'll find anyone who does tell you this, as article 3 section 2, on page 13, specifically precludes the directive from acting as an excuse to toll, stating categorically "it shall concern only the method of collecting tolls or fees".
That said, section 8 does make mention of road charging policies. As these will be at member state level, it's got nothing to do with the EU, and everything to do with your parliament. You must do everything you can to stop these from being implemented, and sooner rather than later. You stopped the Poll tax, but let it be replaced by the much more inequiatble council tax. Stop this before it starts.