Sure, bikes are not as popular, due to public transport, but people who like biking, have many opportunities to enjoy them in places like parks (there's shitload of them), streets that do not see much car traffic, or away from the busiest parts of the city.
It's possible to take a bike onto the public transport (PID/PIT - Prague Integrated Transport).
The thing includes:
Metro, free of charge;
Suburban trains, free of charge (zones P, 0, B), with ticket (zones 1–7), capacity depending on train: basic, extended, or even dedicated bicycle cars on non-working days during the season (line S88);
Trams, only on selected sections, outside of core hours on working days, on direction away from the centre, free of charge (if I'm not mistaken, all these directions go uphill);
Busses, no bikes; exceptions: line 147 during season (April-October), line AE (Airport Express) only bikes prepared for air transport, both free of charge;
Cyklobus, dedicated bike bus, only during season, 16 CZK ($0.70), pic related;
Funicular & Ferries, free of charge.
Full map for bike transport in Prague: https://ropid.cz/wp-content/uploads/mapy/schemata-trvala/a5_cyklo_doprava.pdf
It's possible to transport a folding bike, as if it was luggage, 16 CZK ($0.70).
I have seen some people biking behind trams, too.
PID also offers B+R (Bike+Ride), besides P+R (Park+Ride), so people can leave their bikes near metro and suburban train stations, free of charge (there's also something about locking for 20 CZK/$0.87, but I don't exactly understand how it works).
The governing bodies of Prague actively work on promoting biking. They plan on having 5~7% of total PAX in Prague travelling by bikes during summer, 2~3% during winter by 2020, as part of some national programme.