There is no getting around the fact that science costs a great deal of money. The problems begin when scientists agree to accept money from organizations and people that have an agenda, hidden or open. For example, a pharmaceutical company might fund a project that is meant to show the efficacy of a drug it has developed. The scientists who are testing the drug are perfectly aware of their source of funding, and even if they are honest scientists, they are subtly influenced by that funding source to get results that are favorable to the funding source.
In other instances, government money is available, and one would think that there would be no risk of bias, but even in those cases, federal funding has sometimes been provided in pursuit of a political agenda. One example might be the morning-after pill, which, if taken quickly enough, prevents pregnancy from developing. For anti-abortion activists, this is considered a form of abortion and is avidly opposed by them. If a study were being conducted on the risks of this pill, what do you imagine the outcome would have been if the study were funded by the Bush administration? What might the outcome be if such a study were funded by the Obama administration, which is a pro-choice administration? Even theoretically unbiased funding sources might be biased and affect the outcome of a study in quite subtle ways.
Because of these difficulties with funding sources, good science is always verified by others. If the results are not replicable, there is no conclusion that can be drawn. This is one way the scientific community tries to solve this problem. Another way to address this problem is to require that all funding sources be disclosed, and I have included for you a link to an article that discusses that prospect.
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