Low cost carriers usually operate from no-frills budget terminals which are designed for quick aircraft turnaround, faster passenger connections with minimal inter-gate passenger transfer times. Such operations are highly sensitive to factors such as aircraft delays, turnaround time and flight connection time and may lead to missed connections for self-connecting transfer passengers. In this paper, we propose a passenger-centric model to analyze the effect of turnaround times, minimum connection times and stochastic delays on missed connections of self-connecting passengers. We use Singapore Changi International Airport Terminal 4, which mainly caters to budget/low cost carriers, as a case study to demonstrate the impact of operational uncertainties on these passenger connections, considering an optimal gate assignment by using heuristic search for scheduled arrivals. The proposed model also incorporates reassignment of gates in the disrupted scenario to minimize spatial deviation from the optimized gate assignments. Results show that the chances of missed connections can be significantly reduced by operationally maintaining higher turnaround time and minimum connection time and by bringing down delays at the airport. Specifically, by maintaining the flight turnaround time at 50 min, minimum connection time at 60 min and by containing arrival delays within 70% of the current delay spread at Terminal 4, transfer passenger missed connections can be prevented for almost all the flights. The gate assignment method adopted in this study is generic and may help to identify the gates, which are more prone to missed connections given operational uncertainties under different flight scenarios.