Semantic segmentation has achieved huge progress via adopting deep Fully Convolutional Networks (FCN). However, the performance of FCN based models severely rely on the amounts of pixel-level annotations which are expensive and time-consuming. To address this problem, it is a good choice to learn to segment with weak supervision from bounding boxes. How to make full use of the class-level and region-level supervisions from bounding boxes is the critical challenge for the weakly supervised learning task. In this paper, we first introduce a box-driven class-wise masking model (BCM) to remove irrelevant regions of each class. Moreover, based on the pixel-level segment proposal generated from the bounding box supervision, we could calculate the mean filling rates of each class to serve as an important prior cue, then we propose a filling rate guided adaptive loss (FR-Loss) to help the model ignore the wrongly labeled pixels in proposals. Unlike previous methods directly training models with the fixed individual segment proposals, our method can adjust the model learning with global statistical information. Thus it can help reduce the negative impacts from wrongly labeled proposals. We evaluate the proposed method on the challenging PASCAL VOC 2012 benchmark and compare with other methods. Extensive experimental results show that the proposed method is effective and achieves the state-of-the-art results.