How do we fix it so that journalists can again be the 'trusted guides' they used to be?
If you are going to write about science and want the public to trust what you are saying to them then you need to understand three simple facts.
fact #1 Many scientists lack basic language skills
Every discipline has its own jargon, and many jargon words mean different things to different scientists. It's the same with math and abbreviations. E can be Young's modulus, Energy or Volts. Avoid ambiguity by not sinking to the same language level as your pet scientist. They may think it is smart to communicate in single letter grunts, bar charts and squiggly lines, but you and your readers have a better command of decent grammar and are much more smarterer, so you get to use real language.
It helps in turning a science paper or press release into something your readers can get their teeth into if you convert it into real language. Now, you may not know this, but scientists use plain language in their leisure time, so that is the time when you should buttonhole them and ask what on earth they were babbling on about when they said: "... our data are conclusively inadequately deparameterised in the region of concern, however we believe that ..."
fact #2 Science deals with facts
Sooner or later some idiot is going to suggest that you check your facts. Ignore them. You get facts from scientists, right? Ok, it is their facts you need to check, not yours. If you see that sources are quoted in a paper - check the facts! Who said "In politics, nothing happens by accident. If it happens, you can bet it was planned that way."? If anyone tells you "Franklin D. Roosevelt. " check their facts. If all else fails, check with James Randi or Wikipedia. Don't bother with Youtube - it's too difficult to embed it in newsprint.
For every so-called fact you will find a counterfact. A good grounding in fundamental physics helps sort the Chase's Cherry Mash from the Schwarzwälder Kirschtorte. If you can't tell who is telling big ones, tell both sides of the story with equal fairness. Aude alteram partem - hear both sides - is as good a maxim for science as it is for law. This doesn't mean that a lawyer can spend all day explaining to the judge how his client was kidnapped by purple pixies from planet poopoo.
Learn to tell fact from opinion. If your source is a guest blog or an op-ed piece then that might indicate a hint or two of not entirely unbiased opinion. You should no more expect a press release from East Anglia University to be gushing with praise about Marc Morano than you should expect Lubos Motl to kiss Al Gore and hand him a garland of flowers.
fact #3 Its all to do with the weather
Whatever you write about during the current global warming / climate change feeding frenzy will be seized on as having implications for the climate debate agendists on both sides. Ancient Egyptians invented the water pump? They had to: climate change. Ancient sediments show CO2 at 2000ppm: climate change. NASA launch delayed due to condensation in janitor's coffee machine: climate change. Ancient manuscript still not decoded, what secrets may it reveal? Climate change! British MP in expenses fraud scandal makes claim for cleaning out moat - climate change!
Climate change is probably the most fiercely debated topic ever in the entire history of science. If you can cover that can of worms in an entirely unbiased, honest and ethical manner then you're a better science writer than I am Gunga_Din!