The Mk IV tank for example weighed 29 tons while having only 12 mm of armor at best. Was the armor layout less "rational" than what came afterwards (for example did they use a lot of armor on the roof or rear?), or did the engine, transmission and tracks weigh so much more that little could be spared for the armor?
Even between the wars the Vickers Independent was extremely poorly armored for it's weight.
It comes down to size and volume. The more volume the tank takes up, the more metal it takes to encase that volume. The metal takes weight.
A MkIV is a large tank, and it's got a huge amount of space to enclose. If you think about the 'surface area' of armor, then imagine the weight of metal required to make even a third of an inch thick all the way around. Then imagine you had much less volume to protect (because you have a smaller crew, and more efficient layout). The same weight of metal is going to cover less surface area, and thus can be thicker. It's part of the reason for the move towards autoloader tanks these days: With one less crewman, volume for one less crewman is necessary, which means that for the same overall weight, a tank can be more thickly protected, or else the tank can overall become lighter.
Even the weight of the tracks is significant. There is more run of track on a WW1 MkIV, all the way up over the top of the vehicle, than there is on a WW2 tank. Track weight is a factor in tank design many people forget becomes seriously thought about. It is for this reason that US tanks tended to have narrower tracks than many of its opponents. Thinner track results in less weight of metal going around, which means the engine can spin those tracks faster, as well as allowing more weight for other things (such as armor) in the same overall weight limit for the vehicle.
To answer your question i will compare the MKIV to the WW2 Cromwell IV, i know the tanks are separated by 20 or so years but hopefully the points i'm making will still stand.
The British Mark IV had an Operating weight of roughly 28 tons /25,401kg (With the female variant being lighter at 27.5 tonnes) with a maximum armour thickness of 12.00mm on the front, 6mm at the rear and 8 at its flanks.
To compare, the British Cromwell IV which is a similar weight at 28.33 tons, had a maximum thickness of 101mm with similar downgrades for side and rear.
The Mk IV was also considarable larger than simliarly weighted tanks that would follow it, at 8.05m in length, 4.12m in width and 5.54m in height. The Cromwell IV by comparison was only 6.50m in length, 3.05m in width and 2.36m in height.
Its engine, a Daimler 6-cylinder, in-line, double sleeve-valved beast, was only capable of producing 105bhp with a top speed of 3.7 Mph (on roads). This would prevent the tank from being extensivly armoured as the increased weight would drastically effect the already low top speed. Again comparing it to the Cromwell IV which had a 600bhp engine and could achieve speeds of 32Mph (on roads)
Due to the low power of the engine and the size of the tank it only makes sense that they had to reduce the armour of the tank in order to make the tank practical for battlefield use. Its already slow speed meant that it was a target for artillary and further slowing it would increase the danger to the tank despite the thicker armour. Also tanks were still new tech at this point, the armours primary role was to protect the crew from small arms fire so they could fulfil their role as an infantry support tool.
Sources - http://www.tankmuseum.org/museum-online/vehicles/object-e1972-63 http://www.tankmuseum.org/museum-online/vehicles/object-e1949-342 http://www.tanks-encyclopedia.com/ww1/gb/tank_MkIV.php
Edit grammar and sources.