Policies are based on risk analysis.
Not all lithium batteries are the same or pose the same risk. The risk from Lithium-ion is different than the risk from Lithium-metal. E-cigarettes are yet another risk category since they involve non-typical batteries and heating elements.
The risk of a serious accident from typical consumer Lithium-ion batteries installed in devices such as laptops, cell phones, etc., and carried onboard the cabin is extremely low. They are everywhere. With millions of flights (and billions of li-ion carrying passengers) each year, to my knowledge there hasn't been a single accident due to a li-ion battery in carry-on baggage.
Lithium-metal batteries, however, are more risky, especially when they are not installed in a device, shipped in bulk, and placed in the cargo compartment. They are considered Dangerous Goods and there are international regulations governing their shipment on planes.
E-cigarettes use a non-typical battery packaging which make them more prone to failure. They are also easy to overcharge, which damages the battery. (In fact around 80% of e-cigarette fires occurred during charging.) And many e-cigarette smokers tamper (modify) the devices to increase their power output, putting even more stress on the battery.
E-cigarettes are banned from checked luggage and may not be charged in flight. Most airlines also ban their use in flight.