The absolute value of sin(x) is used in the integral of cot(x) to ensure the logarithm remains defined, as ln(sin(x)) is not defined when sin(x) is less than or equal to zero. This requirement is linked to the domains of cot(x) and sin(x). The absolute value ensures that the argument of the logarithm is always positive, allowing for valid integration. The discussion emphasizes the importance of considering the behavior of sin(x) in relation to the logarithmic function. Understanding these domain restrictions is crucial for proper evaluation of the integral.