Modern deep neural networks are able to beat human annotators in several medical image processing tasks. In practical manual annotation for medical image segmentation tasks, the labels of annotators often show inter-observer variability (IOV) which is mainly caused by annotators' different understandings of expertise. In order to build a trustworthy segmentation system, robust models should consider how to capture uncertainty in samples and labels. Different from the conventional way of handling IOV with label fusion such as majority voting, a fuzzy integral based ensemble framework of multiple deep learning models for optic disc segmentation is proposed. Each component segmentation model is trained with respect to an annotator. Then, a powerful nonlinear aggregation function, the Choquet integral, is employed in form of a neural network to integrate the segmentation results of multiple annotators. The proposed method is validated on the public RIM-ONE dataset consisting of 169 fundus images and each image is annotated by 5 experts. Compared with conventional segmentation ensemble methods, the proposed methods achieves a higher Dice score (98.69%).