A taxi from Madrid airport to Madrid Atocha station is a fixed fare of €30, and no tipping is expected beyond this. I have no idea what a taxi from the airport all the way to Toledo would cost.
Atocha station is indeed confusing and hard to navigate - and I'm used to New York Penn Station! As acraven says, that just means you can't allow only 5 minutes to change trains. Your train from the airport is a cercanias, and arrives at the cercanias part of the station. Your train to Toledo is an AVE, but here's where it gets complicated - there are AVE departures from upper and lower levels, and neither one is near the cercanias area. At least in 2015, the train from Atocha to Toledo left from the lower AVE level; by mistake I went to the upper AVE departures area, and had to find my way to the lower level. I couldn't find elevators or escalators and had to drag my bags (bigger ones than I use now, alas) down the stairs.
The other issue with Atocha station is that the ticket buying lines can be very long. However, as acraven says, you can buy your tickets for both parts (airport to Atocha and Atocha to Toledo) while at the airport. Tickets in hand, and knowing you have to look for the lower level AVE departures, you should be fine. Do ask IMMEDIATELY if you are at all lost or unsure - don't waste time, and don't make my mistake of not asking for elevators (I'm sure they have them somewhere).
Note that you have to go through a security check to get to the AVE trains. Your bags are X-rayed, but it's not nearly as intrusive as an airport screening. Also, they close the doors on AVE trains a few minutes before departure. These two factors mean that you can't jump on an AVE just as it's departing - yet more reason to allow some time between your scheduled arrival at Atocha and your departure. If you're early for your train to Toledo, you will wait in a lounge, where there are seats, snacks, bathroom, etc.
If you do want to take a taxi, I can say I've never had a problem with taxis in Spain (more than I can say for some countries). They use the meter (unless it's a fixed fare such as from the airport to the center of Madrid), and extra charges are clearly posted on a placard in the taxi (such as for putting items in the trunk, extra passengers, leaving from train stations, etc). So, I see no need to use another company.
Why not ask your Toledo hotel about how much a taxi will cost from the airport, or they can arrange a car for a better price? You always have the option to decline if their price is higher.