How can cells stop diffusion through protein channels?

Well there are many different factors that might dictate whether or not a molecule is capable of passively (diffusion) crossing the threshold of the phosolipid bi-layer (cell membrane). The size would be one variable. If it is too large, it might require assistance to cross over. The polarity of the molecule as it might interact negatively (no pun intended) with the polarity of either the cell membrane or the cell entirely, if it contains large amounts of opposing ions. And then, of course, the concentration gradient of the molecule and how much of this same molecule exists in and outside the cell itself. If any of these obstacles exists, the molecule would require active transport into the cell, which means it would require the expenditure of energy, or a pump or gateway of some kind, depending on the substance...