For driving from Delft to Bruges you can take the following route: From Rotterdam take A15 west to Europoort and exit to N57 / Brielle / Middelburg. This is the route along the coast with (former) islands, dams, causeways and charming places worth to visit. No worries about ferries, the few in service are only for bikers and foot passengers.
Brielle is nice and worth visiting as well as tiny but very charming Goedereede. Further south you will drive over the impressive Eastern Scheldt Storm Surge Barrier. Certainly not to miss is Veere and actually Middelburg too. From the latter follow N254 south-east to the Westerschelde tunnel / Terneuzen, but keep following the freeway till the exit to N61 / Oostburg / Noordzeekust at the southside of the tunnel. Keep driving west to Oostburg and Sluis till you see Brugge (Bruges) is signposted.
Sluis is lovely and nearby Sint-Anna-ter-Muiden too. Later you can follow the freeway to Bruges or drive through the much more scenic countryside to Oostkerke and Damme, with the final leg to Bruges along the old canal.
With six hours and picking up the rental car and possible traffic jams around Rotterdam there will be not much time left to visit one of the mentioned places. So if possible add several hours for the drive. Neverhteless you need to make a selection. My pick would be Goedereede, Veere, Middelburg, Sint-Anna-ter-Muiden and the final leg through the countryside to Bruges.
In Bruges I often park my car next to the railway station, prices are reasonable and safe during the day, however not sure during the night. You can streetpark outside the historical centre, nevertheless best is asking your hotel or B&B for the best and safest options.
On the way back you can go through the tunnel again and visit very charming Zierikzee. There are free parkings, one south of the historic centre at an easy walking distance from the Zuidhavenpoort. You can combine Zierikzee with Middelburg for instance if there is not enough time during the other drive. If of interest you can include the Flood Disaster Museum in nearby Ouwerkerk and / or closer to Rotterdam Willemstad. Maybe a good place for dinner?
If hydraulic engineering is of interest, this area is world famous for it’s Delta Works with the before mentioned storm surge barrier and the Maeslant Barrier west of Rotterdam as highlights. The latter has a small but informative visitor centre offering guided tours, from which a few in English. There will be no time for it, but I think worth mentioning.
So there is a lot to see and do. Anyway to my opinion it’s worth driving in this case. Some car rental agencies are open 24/7 and give more room dropping the car later then during the usual office hours. Later in the evening the traffic jams arround Rotterdam and the freeway to Leiden are for the most part gone. For the frist day you can consider taking the train from Delft to Rotterdam (needs a ½ hour) for picking up for instance the rental car to avoid the traffic jams there as much as possible. For this journey you don’t need much luggage, see if you can store some of it somewhere and pick it up later. Gives more flexibility if travelling with the train is needed. Many railway stations have lockers, even for the bigger suitcases.