Inaccurate tool localization is one of the main reasons for failures in automating surgical tasks. Imprecise robot kinematics and noisy observations caused by the poor visual acuity of an endoscopic camera make tool tracking challenging. Previous works in surgical automation adopt environment-specific setups or hard-coded strategies instead of explicitly considering motion and observation uncertainty of tool tracking in their policies. In this work, we present SURESTEP, an uncertainty-aware trajectory optimization framework for robust surgical automation. We model the uncertainty of tool tracking with the components motivated by the sources of noise in typical surgical scenes. Using a Gaussian assumption to propagate our uncertainty models through a given tool trajectory, SURESTEP provides a general framework that minimizes the upper bound on the entropy of the final estimated tool distribution. We compare SURESTEP with a baseline method on a real-world suture needle regrasping task under challenging environmental conditions, such as poor lighting and a moving endoscopic camera. The results over 60 regrasps on the da Vinci Research Kit (dVRK) demonstrate that our optimized trajectories significantly outperform the un-optimized baseline.