The appearance difference between cypress and western red cedar is largely subjective and is only noticeable if you use a clear wood finish rather than a stain or paint. Despite the name, western red cedar has a golden brown color. Cypress is a tan wood that can have a slight reddish tint. The grain patterns are usually fairly consistent straight patterns for both types of wood, but this varies based on the grade of the wood.
Both cypress and western red cedar are used for fencing because they can withstand the punishment of the elements better than most varieties of wood. Both share similar resistances to rot and vermin, which should make both of these problems little to no issue for the life of the fence. Cypress has better structural integrity than western red cedar, but this is not actually relevant to a fence. The wood used on a fence does not carry much, if any, weight with normal use. Western red cedar should be more than adequate for any fence under normal conditions.
The price of wood can vary significantly based on the demand and location. Generally, western red cedar is going to be cheaper than cypress in almost every situation. The amount of the price difference does vary significantly. In the Southeastern United States, where cypress is most commonly grown, there is usually little to no price difference. However, in other regions, the price of cypress rises significantly, while the price of western red cedar is fairly consistent. In some situations, cypress can cost more than double what western red cedar costs.
For most people, western red cedar is the better choice for a fence. The extra strength that cypress has is not relevant for a fence and does not justify the additional cost for most people. In the Southeastern United States, where cypress is potentially near the same price as western red cedar, cypress might be the better choice. Although the strength increase should not be important, western red cedar does not have any extra benefit over cypress once the cost difference is removed.