For a trip in September to Portugal, does anyone know the best means for getting from the Lisbon airport to the town of Coimbra? I am excluding car rental as an option.
Must one go to the train station? Or are there reliable and secure modes of transport directly from the airport?
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I recommend the train. And it's fairly easy.
Just take a taxi down to the train station "Lisboa Oriente" or "Gare do Oriente in Portuguese" which is 5 minutes by taxi from the airport. (I recommend to take the taxi in front of departures for this short hop, instead of arrivals as taxi drivers are not very keen on this "too short" route).
The fastest train (Alfa Pendular) takes 1:33 and costs 22.50EUR.
The slightly slower train (Intercidades) takes ~1:50 and costs 19.00EUR.
You can check the schedule here
On the left side fill in the from field as Lisboa - Oriente and the to field as Coimbra-b
The train station in Coimbra-b is not in the very center of town but you can take a 5 minute connecting train to Coimbra-a which is in the center (your ticket from Lisbon should cover that 5 minute connection). Or a quick taxi ride to wherever you need to go.
The Metro connection from LIS airport to Gare do Oriente may be open in September. I'll do a quick check and post if that's the case.
Enjoy Coimbra. Wonderful place full of history. Make sure you visit the University Library.
Just take a taxi down to the train station "Lisboa Oriente" or "Gare do Oriente in Portuguese" which is 5 minutes by taxi from the airport. (I recommend to take the taxi in front of departures for this short hop, instead of arrivals as taxi drivers are not very keen on this "too short" route).
The fastest train (Alfa Pendular) takes 1:33 and costs 22.50EUR.
The slightly slower train (Intercidades) takes ~1:50 and costs 19.00EUR.
You can check the schedule here
On the left side fill in the from field as Lisboa - Oriente and the to field as Coimbra-b
The train station in Coimbra-b is not in the very center of town but you can take a 5 minute connecting train to Coimbra-a which is in the center (your ticket from Lisbon should cover that 5 minute connection). Or a quick taxi ride to wherever you need to go.
The Metro connection from LIS airport to Gare do Oriente may be open in September. I'll do a quick check and post if that's the case.
Enjoy Coimbra. Wonderful place full of history. Make sure you visit the University Library.
GBM
Just to supplement this excellent advice, if the Metro connection isn't yet open and you would prefer not to take a cab, there's also a frequent bus service between the airport and this train station. From memory, I think it's #750? I've down this hop with moderate luggage (one checked rolling bag and one carry-on) and had no problem. It's a 10-15 minute trip, with departures about every 10 minutes. Fare was, I think, maybe 1,25 EUR? I don't think it was more than 2,5 EUR.
I haven't done this trip since 2009, so double-check the details if you can. (I'll try to double-check, too.) Enjoy Coimbra, and the rest of Portugal! Coimbra is a lovely city, and Portugal is one of my favorite countries in the whole world.
The metro extension to the airport is opening 3 JUL with 99.9% certainty this time ). The only bus that goes directly from the airport is 44 and it doesn't run that often. A metro ticket is 1.25€+0.50€ cost of a rechargeable card, a cab shouldn't be more than 5-6€ with luggage (so if you have more than 3 people it's probably worth to cab it). Just make sure the driver does not turn on tarifa 3 (aka the tourist tariff).
Take the metro 3 stops to Oriente go 3 levels up, buy your ticket and go one more level up to track 1 and board the train. There's Alfa and Intercity trains. Either one will do the trick, as the ride is less than 2 hrs.
If you want, you can buy your ticket online at www.cp.pt (the only benefit to that is that you can select seats). Once you buy your ticket you can only exchange it up to 30 mins before the train departs its origin, so in your case it would be better to buy it on arrival.
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The high-speed rail from LIS made me feel mildly queasy - it leans noticeably into the relatively tight radius turns. It's a good value for intercity travel in Portugal.
Be very cautious at the main station in Lisbon. Pickpockets and thieves constantly case the joint. I saw two separate teams doing this the last time I was there. One guy went in and out the bathrooms on a three minute cycle, while one of his accomplices matched the cycle by walking through the waiting room. If your bag is not lassoed to your body, it could be lifted very quickly.
The high-speed rail from LIS made me feel mildly queasy - it leans noticeably into the relatively tight radius turns. It's a good value for intercity travel in Portugal.
Be very cautious at the main station in Lisbon. Pickpockets and thieves constantly case the joint. I saw two separate teams doing this the last time I was there. One guy went in and out the bathrooms on a three minute cycle, while one of his accomplices matched the cycle by walking through the waiting room. If your bag is not lassoed to your body, it could be lifted very quickly.
The most covenient station for LIS is Gare do Oriente, not the main station of Santa Apolonia.
). The only bus that goes directly from the airport is 44 and it doesn't run that often. A metro ticket is 1.25€+0.50€ cost of a rechargeable card, a cab shouldn't be more than 5-6€ with luggage (so if you have more than 3 people it's probably worth to cab it). Just make sure the driver does not turn on tarifa 3 (aka the tourist tariff). 
