Physical layer security has recently been regarded as an emerging technique to complement and improve the communication security in future wireless networks. The current research and development in physical layer security is often based on the ideal assumption of perfect channel knowledge or the capability of variable-rate transmissions. In this work, we study the secure transmission design in more practical scenarios by considering channel estimation errors at the receiver and investigating both fixed-rate and variable-rate transmissions. Assuming quasi-static fading channels, we design secure on-off transmission schemes to maximize the throughput subject to a constraint on secrecy outage probability. For systems with given and fixed encoding rates, we show how the optimal on-off transmission thresholds and the achievable throughput vary with the amount of knowledge on the eavesdropper's channel. In particular, our design covers the interesting case where the eavesdropper also uses the pilots sent from the transmitter to obtain imperfect channel estimation. An interesting observation is that using too much pilot power can harm the throughput of secure transmission if both the legitimate receiver and the eavesdropper have channel estimation errors, while the secure transmission always benefits from increasing pilot power when only the legitimate receiver has channel estimation errors but not the eavesdropper. When the encoding rates are controllable parameters to design, we further derive both a non-adaptive and an adaptive rate transmission schemes by jointly optimizing the encoding rates and the on-off transmission thresholds to maximize the throughput of secure transmissions.