There is definitely a toll on I-75/Alligator Alley between Naples and west Broward (Ft. Luaderdale). It's currently $3 each way. Ft. Lauderdale is about 30 miles north of where US 41 comes into Miami, so you'll need to take one of several roads south from there. If you take the Florida's Turnpike extension, which has the least traffic of the three, that will be another $1.50 toll.
I-75 is a divided, high-speed road with the same design standards as the rest of U.S. interstates. There are multiple lighted rest areas with restrooms and basic services. There is food and fuel at the Miccosukee reservation truck stop about halfway across.
U.S. 41 is built to pre-Interstate standards, two lanes undivided, with minimal shoulders. There are no services or rest areas. The last 15 miles or so into Miami are heavily suburban and traffic gets bad.
Even though it's a shorter trip via U.S. 41, I haven't taken it since Alligator Alley was finished. I'm no fan of long stretches of undivided roads.
