The article published in Nature mentions fraud as one of the potential causes for the lack of reproducibility, but it's not the only one mentioned and not even the most common answer from the survey.
The article specifically says:
The survey asked scientists what led to problems in reproducibility. More than 60% of respondents said that each of two factors — pressure to publish and selective reporting — always or often contributed. More than half pointed to insufficient replication in the lab, poor oversight or low statistical power. A smaller proportion pointed to obstacles such as variability in reagents or the use of specialized techniques that are difficult to repeat.
There are many problems in the scientific world (fraud being one of them in many cases, for sure), but that doesn't mean science is not reliable anymore or that the scientific method is dead. We just have to be cautious with results that have not been verified by multiple sources and we need to find ways to promote and fund replication studies.
You should read the Wikipedia entry for Replication Crisis if you're really interested in this issue.