Smaller non-profits are _way_ more likely to poorly use your funds, especially if they fundraise. Use charity navigator or other reputable organizations to see if a charity you want to support uses your funds well or not.
Some non-profits only pay salaries of employees, but spend the vast majority of their time and money on their fundraising events, which are just ways for rich people to throw parties for free. In that case, they'd still pass your test.
People who work at non-profits deserve to be paid a similar salary to what they'd be paid in the private sector. The important part is that a non-profit should be using the majority of their funds on their mission (and that may require the majority of the funds going to the workers, depending on the mission).