It is counter intuitive though precisely because the pennies analogy doesn’t work.
If I put a 1m stack of quarters on a pressure gauge, then I put one quarter on the gauge and a stack of pennies on top of it up to 1m high, I get two different readings. Conversely if I measure the pressure at the bottom of two bottles the same shape as the stacks of coins, I get the same readings.
In case it was not clear in my analogy a "penny" (it can be anything solid and incompressible) is representative of a water molecule. If you want to compare the pressures of stacks of pennies and quarters because for some reason you are fixated in these specific physical coins rather than what they represent then I will make it explicit. Imagine pennies represent water and quarters represent mercury. Two different liquids, two different coins, two different pressures. I don't get what you guys don't get.
Can you explain to me why you think it is intuitive that the downward pressure of a liquid at the bottom of a container should vary for equal depths but different volumes? E.g. you seem to intuitively think that if you have a big pan filled with 1 inch of water the water pressure at the bottom of the pan is greater than the pressure at the bottom of a 50 ml flask also filled with one inch of water. This is false but I am interested as to why you and the others think it is "intuitive?" Where does the additional force come from to increase the pressure in the bigger pan? Gravity pulls straight down.
If you have a bottle of 1 kg of water and put it on a plank between two stools, what matters to know if the plank will break is the total weight (and torque) of the bottle and the surface of contact. The shape of the bottle is irrelevant.
When you have that image in mind and someone suddenly tells you that actually no, 1 kg of water on a 50 meters high column can actually break things 1kg of water in a bucket can't, it is very counterintuitive.
And the stack of pennies is really unhelpful I feel. Make an inverse pyramid with 1000 pennies, all of them resting on one at the bottom tip, or make a column of these, the force exerted on the bottom one will be the same. The force per area as well. Not so with water.
The difference is that the water molecules move until they find an equilibrium in which there is a gradient of pressure and where molecules push back in every direction equally. Pennies do not, they are content exerting "pressure" in a single direction