This work introduces a hybrid deep learning approach integrated with an Unscented Kalman Filter (UKF) to enhance pose estimation accuracy in Visual-Inertial Odometry (VIO) for autonomous navigation. The proposed model employs a Vision Transformer (ViT) network to effectively capture temporal dependencies from inertial measurement unit (IMU) data and utilizes a Multiscale Convolutional Neural Network (MCNN) to learn optical flow-based motion cues from visual data. An adaptive sensor fusion module dynamically weights IMU and visual features by leveraging estimated uncertainty, thus improving robustness in diverse and challenging environmental conditions. Additionally, a novel uncertainty-aware loss function is proposed to explicitly incorporate prediction uncertainty into the learning process, enabling robust and accurate navigation under noisy, incomplete, or unreliable sensor inputs. Comprehensive evaluations of the KITTI dataset demonstrate that the proposed method significantly outperforms baseline approaches, achieving superior performance in terms of Absolute Trajectory Error (ATE) and Relative Pose Error (RPE). The lightweight and computationally efficient model processes data at 155 FPS on an NVIDIA A100 GPU, making it highly suitable for deployment in resource-constrained autonomous systems.