There are materials which are "transparent" to microwaves and don't get hot in the microwave oven but I can't remember which ones. And glass definitely isn't one of them.
The reason why glass vessels become hotter in a microwave oven is because glass has a much higher thermal conductivity than plastic, so it becomes heated from the hot food.
Using two pieces of cloth (e.g. cut from a small towel) to hold the hot glass vessel is enough to take it safely out of the oven and this negligible inconvenience matters much less than the undesirable effects of heating food in a plastic vessel.