According to this article in the current New England Journal of Medicine, physicians are more apt to prescribe drugs supported by studies they perceive as rigorous, than those supported by studies perceived as less rigorous. More interestingly, though, physicians downgrade their perception of the rigor of a study, their confidence in its results, and their willingness to prescribe the studied drug, when the study discloses that it was industry-sponsored. Physicians surveyed were twice as willing to prescribe a drug supported by an NIH study than one supported by an industry-sponsored study.
In general I greet this as good news. Industry sponsorship injects bias into the literature in many ways: via unconscious biasing of sponsored researchers, via careful selection of the kinds of studies sponsored (e.g., avoidance of head-to-head drug comparisons that have any chance of turning out badly), and even (in a few documented cases) via the burial or abandonment of sponsored studies that don't work out. So it's fine if physicians greet industry-sponsored trials with some skepticism.
Two worries, though: first, there can be too much of a good thing. After all, if a company develops a drug that really works, it will want to sponsor studies to prove that fact; and too much skepticism of positive results could end up hurting patients. Second, if industry sponsorship gives rise to skepticism, then there's an incentive to bury the fact of industry sponsorship via ghost authorship or other means.
Study registers, publication of negative results, rigorous authorship standards, rules for disclosure of funding sources and of conflicting interests, public funding for independent research: these can all help.
But the facts are 1) that we rely on private, profit-motivated research to find our new drugs; 2) that such research has historically done an excellent job in discovering and publicizing useful new drugs; and 3) that the very same motives that drive the industry to do a good job in discovering and publicizing useful new drugs are those that drive it to pollute and bias the literature. So there will be no easy answers.