Travelling using a low cost airline Isn't normally a problem but you need to bear in mind that depending on the airport you might not have some facilities.
If you are travelling from Lisbon note, that they have now two separate terminals one for flagship companies and another one for low-cost airlines. The terminal dedicated to low cost airlines is quite crowded and I recommend you to buy some food before getting to the airport as prices are extremely expensive. A sandwich can cost you €11 and doesn't have any quality. To avoid queueing to buy food from very little options get a little snack before getting to the airport : This is the advice of a Portuguese traveler.