Given the amount of malware in the play store, I'm not sure about this...
The point is that F-Droid weakens Android's security model, in other words, F-Droid requires more trust on your part. I think it is reasonable to trust the somewhat niche open source community more than the most popular and therefore the most attacked app store. You may also not want to feed Google, but it doesn't change the fact that F-Droid is technically less secure. The article's debatable suggestion is to get your favorite open source apps you trust from the Play Store to get the best of both worlds.
The article is interesting because most of the points are actually fixable by F-Droid. So it is good to see from a "how to improve F-Droid" angle than "F-Droid sucks".