Within the natural world, cyclohexane molecules are constantly changing with flips and twists to boats and twist boats but it spends the majority of time in the standard chair conformation. Because of this initial experimental observation it can be reasoned that this is the most stable and "preferred" conformation.
Digging a little deeper into why this is the case leads us back to a simpler methane molecule.
Methane, #"CH"_4#, if you remember, has a carbon atom with 4 hydrogen atoms spaced exactly #109.5""^@# from each other to form the perfect tetrahedral molecule.
Now, let's say we bound 6 methane molecules together into a ring but in a way that maintains as close to #109.5""^@# spacing as possible for each atom. This ideal structure that maintains the tetrahedral spacing for each methane is the chair conformation! (The actual bond angles in cyclohexane are #110.9""^@# but this is the closest it can get to #109.5""^@#)